rs199728172

Variant names:

• chr18-26267520-C-A
• rs199728172
• NM_005640.3:c.494C>A

Your query was ambiguous. Multiple possible variants found:

• chr18-26267520-C-A
• chr18-26267520-C-G
• chr18-26267520-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_005640.3(TAF4B):​c.494C>A​(p.Ser165Tyr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: TAF4B NM_005640.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.18

Genes affected

TAF4B (HGNC:11538): (TATA-box binding protein associated factor 4b) TATA binding protein (TBP) and TBP-associated factors (TAFs) participate in the formation of the TFIID protein complex, which is involved in initiation of transcription of genes by RNA polymerase II. This gene encodes a cell type-specific TAF that may be responsible for mediating transcription by a subset of activators in B cells. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jun 2014]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAF4B	NM_005640.3	c.494C>A	p.Ser165Tyr	missense_variant	Exon 3 of 15	ENST00000269142.10	NP_005631.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAF4B	ENST00000269142.10	c.494C>A	p.Ser165Tyr	missense_variant	Exon 3 of 15	1	NM_005640.3	ENSP00000269142.6
TAF4B	ENST00000578121.5	c.494C>A	p.Ser165Tyr	missense_variant	Exon 3 of 15	2		ENSP00000462980.1
TAF4B	ENST00000418698.3	n.494C>A		non_coding_transcript_exon_variant	Exon 3 of 16	5		ENSP00000389365.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.15
BayesDel_addAF	Uncertain	0.032	T
BayesDel_noAF	Benign	-0.19
CADD	Pathogenic	26
DANN	Benign	0.88
DEOGEN2	Uncertain	0.42	T;T
Eigen	Uncertain	0.61
Eigen_PC	Uncertain	0.60
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Benign	0.81	T;T
M_CAP	Benign	0.012	T
MetaRNN	Uncertain	0.63	D;D
MetaSVM	Benign	-0.93	T
MutationAssessor	Uncertain	2.6	M;.
PrimateAI	Benign	0.45	T
PROVEAN	Uncertain	-2.8	D;.
REVEL	Benign	0.12
Sift	Uncertain	0.0040	D;.
Sift4G	Uncertain	0.030	D;D
Polyphen		0.99	D;.
Vest4		0.66
MutPred		0.36		Loss of sheet (P = 3e-04);Loss of sheet (P = 3e-04);
MVP		0.22
MPC		0.28
ClinPred		0.85	D
GERP RS		5.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.26
gMVP		0.37

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.15		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs199728172; hg19: chr18-23847484;