dbSNP rs147865905: TAF2:p.Pro517Pro (chr8-119789609-C-A) – ACMG Classification: Likely_benign (-1 pts)

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7

The NM_003184.4(TAF2):c.1551G>T(p.Pro517Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. P517P) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 32)

Consequence

TAF2
NM_003184.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.229

Publications

2 publications found

Variant links:

Genes affected

TAF2 (HGNC:11536): (TATA-box binding protein associated factor 2) Initiation of transcription by RNA polymerase II requires the activities of more than 70 polypeptides. The protein that coordinates these activities is transcription factor IID (TFIID), which binds to the core promoter to position the polymerase properly, serves as the scaffold for assembly of the remainder of the transcription complex, and acts as a channel for regulatory signals. TFIID is composed of the TATA-binding protein (TBP) and a group of evolutionarily conserved proteins known as TBP-associated factors or TAFs. TAFs may participate in basal transcription, serve as coactivators, function in promoter recognition or modify general transcription factors (GTFs) to facilitate complex assembly and transcription initiation. This gene encodes one of the larger subunits of TFIID that is stably associated with the TFIID complex. It contributes to interactions at and downstream of the transcription initiation site, interactions that help determine transcription complex response to activators. [provided by RefSeq, Jul 2008]

TAF2 Gene-Disease associations (from GenCC):

microcephaly-thin corpus callosum-intellectual disability syndrome
Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE, LIMITED Submitted by: G2P, Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics

TAF2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -1 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (REVEL=0.024).

BP7

Synonymous conserved (PhyloP=0.229 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAF2	NM_003184.4 link	c.1551G>T	p.Pro517Pro	synonymous_variant	Exon 12 of 26	ENST00000378164.7	NP_003175.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein
TAF2	ENST00000378164.7 link	c.1551G>T	p.Pro517Pro	synonymous_variant	Exon 12 of 26	1	NM_003184.4	ENSP00000367406.2
TAF2	ENST00000686879.1 link	c.1551G>T	p.Pro517Pro	synonymous_variant	Exon 12 of 27			ENSP00000509206.1
TAF2	ENST00000685235.1 link	c.1551G>T	p.Pro517Pro	synonymous_variant	Exon 12 of 26			ENSP00000510174.1
TAF2	ENST00000688645.1 link	c.1551G>T	p.Pro517Pro	synonymous_variant	Exon 12 of 25			ENSP00000509978.1
TAF2	ENST00000523904.2 link	c.1437G>T	p.Pro479Pro	synonymous_variant	Exon 11 of 25	3		ENSP00000430832.2
TAF2	ENST00000690144.1 link	c.1551G>T	p.Pro517Pro	synonymous_variant	Exon 12 of 26			ENSP00000510548.1
TAF2	ENST00000685202.1 link	n.1551G>T		non_coding_transcript_exon_variant	Exon 12 of 27			ENSP00000509214.1
TAF2	ENST00000685503.1 link	n.*943G>T		non_coding_transcript_exon_variant	Exon 12 of 26			ENSP00000509198.1
TAF2	ENST00000685663.1 link	n.*1423G>T		non_coding_transcript_exon_variant	Exon 14 of 28			ENSP00000508988.1
TAF2	ENST00000685684.1 link	n.*3018G>T		non_coding_transcript_exon_variant	Exon 11 of 25			ENSP00000509441.1
TAF2	ENST00000685824.1 link	n.*1252G>T		non_coding_transcript_exon_variant	Exon 10 of 24			ENSP00000510262.1
TAF2	ENST00000685876.1 link	n.*1269G>T		non_coding_transcript_exon_variant	Exon 13 of 27			ENSP00000510493.1
TAF2	ENST00000685993.1 link	n.*1366G>T		non_coding_transcript_exon_variant	Exon 11 of 25			ENSP00000510102.1
TAF2	ENST00000686098.1 link	n.*196G>T		non_coding_transcript_exon_variant	Exon 11 of 25			ENSP00000509102.1
TAF2	ENST00000688037.1 link	n.*970G>T		non_coding_transcript_exon_variant	Exon 9 of 23			ENSP00000510169.1
TAF2	ENST00000689164.1 link	n.*196G>T		non_coding_transcript_exon_variant	Exon 10 of 24			ENSP00000508729.1
TAF2	ENST00000689919.1 link	n.*1269G>T		non_coding_transcript_exon_variant	Exon 13 of 26			ENSP00000510768.1
TAF2	ENST00000690808.1 link	n.*787G>T		non_coding_transcript_exon_variant	Exon 12 of 26			ENSP00000509791.1
TAF2	ENST00000690922.1 link	n.1551G>T		non_coding_transcript_exon_variant	Exon 12 of 26			ENSP00000509498.1
TAF2	ENST00000691847.1 link	n.*852G>T		non_coding_transcript_exon_variant	Exon 11 of 24			ENSP00000509663.1
TAF2	ENST00000691880.1 link	n.*1207G>T		non_coding_transcript_exon_variant	Exon 11 of 25			ENSP00000508515.1
TAF2	ENST00000692518.1 link	n.*1252G>T		non_coding_transcript_exon_variant	Exon 10 of 25			ENSP00000508959.1
TAF2	ENST00000692707.1 link	n.*1419G>T		non_coding_transcript_exon_variant	Exon 14 of 28			ENSP00000509024.1
TAF2	ENST00000692916.1 link	n.*938G>T		non_coding_transcript_exon_variant	Exon 11 of 25			ENSP00000509603.1
TAF2	ENST00000685503.1 link	n.*943G>T		3_prime_UTR_variant	Exon 12 of 26			ENSP00000509198.1
TAF2	ENST00000685663.1 link	n.*1423G>T		3_prime_UTR_variant	Exon 14 of 28			ENSP00000508988.1
TAF2	ENST00000685684.1 link	n.*3018G>T		3_prime_UTR_variant	Exon 11 of 25			ENSP00000509441.1
TAF2	ENST00000685824.1 link	n.*1252G>T		3_prime_UTR_variant	Exon 10 of 24			ENSP00000510262.1
TAF2	ENST00000685876.1 link	n.*1269G>T		3_prime_UTR_variant	Exon 13 of 27			ENSP00000510493.1
TAF2	ENST00000685993.1 link	n.*1366G>T		3_prime_UTR_variant	Exon 11 of 25			ENSP00000510102.1
TAF2	ENST00000686098.1 link	n.*196G>T		3_prime_UTR_variant	Exon 11 of 25			ENSP00000509102.1
TAF2	ENST00000688037.1 link	n.*970G>T		3_prime_UTR_variant	Exon 9 of 23			ENSP00000510169.1
TAF2	ENST00000689164.1 link	n.*196G>T		3_prime_UTR_variant	Exon 10 of 24			ENSP00000508729.1
TAF2	ENST00000689919.1 link	n.*1269G>T		3_prime_UTR_variant	Exon 13 of 26			ENSP00000510768.1
TAF2	ENST00000690808.1 link	n.*787G>T		3_prime_UTR_variant	Exon 12 of 26			ENSP00000509791.1
TAF2	ENST00000691847.1 link	n.*852G>T		3_prime_UTR_variant	Exon 11 of 24			ENSP00000509663.1
TAF2	ENST00000691880.1 link	n.*1207G>T		3_prime_UTR_variant	Exon 11 of 25			ENSP00000508515.1
TAF2	ENST00000692518.1 link	n.*1252G>T		3_prime_UTR_variant	Exon 10 of 25			ENSP00000508959.1
TAF2	ENST00000692707.1 link	n.*1419G>T		3_prime_UTR_variant	Exon 14 of 28			ENSP00000509024.1
TAF2	ENST00000692916.1 link	n.*938G>T		3_prime_UTR_variant	Exon 11 of 25			ENSP00000509603.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.28

CADD

Benign

5.6

(source)

DANN

Benign

0.63

PhyloP100

0.23

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over