17-35820316-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_139215.3(TAF15):​c.185-16C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000916 in 1,613,196 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0042 ( 3 hom., cov: 32)
Exomes 𝑓: 0.00058 ( 1 hom. )

Consequence

TAF15
NM_139215.3 intron

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.518
Variant links:
Genes affected
TAF15 (HGNC:11547): (TATA-box binding protein associated factor 15) This gene encodes a member of the TET family of RNA-binding proteins. The encoded protein plays a role in RNA polymerase II gene transcription as a component of a distinct subset of multi-subunit transcription initiation factor TFIID complexes. Translocations involving this gene play a role in acute leukemia and extraskeletal myxoid chondrosarcoma, and mutations in this gene may play a role in amyotrophic lateral sclerosis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, May 2012]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 17-35820316-C-T is Benign according to our data. Variant chr17-35820316-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1300617.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.000579 (846/1460954) while in subpopulation AFR AF= 0.0162 (541/33462). AF 95% confidence interval is 0.015. There are 1 homozygotes in gnomad4_exome. There are 393 alleles in male gnomad4_exome subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 632 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TAF15NM_139215.3 linkc.185-16C>T intron_variant ENST00000605844.6 NP_631961.1 Q92804-1
TAF15NM_003487.4 linkc.176-16C>T intron_variant NP_003478.1 Q92804-2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TAF15ENST00000605844.6 linkc.185-16C>T intron_variant 1 NM_139215.3 ENSP00000474096.1 Q92804-1

Frequencies

GnomAD3 genomes
AF:
0.00413
AC:
628
AN:
152124
Hom.:
3
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0138
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00177
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000191
Gnomad OTH
AF:
0.00718
GnomAD3 exomes
AF:
0.00117
AC:
295
AN:
251284
Hom.:
1
AF XY:
0.000854
AC XY:
116
AN XY:
135828
show subpopulations
Gnomad AFR exome
AF:
0.0141
Gnomad AMR exome
AF:
0.00121
Gnomad ASJ exome
AF:
0.000595
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000114
Gnomad OTH exome
AF:
0.000490
GnomAD4 exome
AF:
0.000579
AC:
846
AN:
1460954
Hom.:
1
Cov.:
32
AF XY:
0.000541
AC XY:
393
AN XY:
726836
show subpopulations
Gnomad4 AFR exome
AF:
0.0162
Gnomad4 AMR exome
AF:
0.00116
Gnomad4 ASJ exome
AF:
0.000345
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000165
Gnomad4 OTH exome
AF:
0.000828
GnomAD4 genome
AF:
0.00415
AC:
632
AN:
152242
Hom.:
3
Cov.:
32
AF XY:
0.00388
AC XY:
289
AN XY:
74434
show subpopulations
Gnomad4 AFR
AF:
0.0138
Gnomad4 AMR
AF:
0.00177
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000191
Gnomad4 OTH
AF:
0.00710
Alfa
AF:
0.00181
Hom.:
0
Bravo
AF:
0.00539
Asia WGS
AF:
0.000577
AC:
2
AN:
3478

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingGeneDxNov 05, 2020- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
CADD
Benign
9.1
DANN
Benign
0.54

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs147370557; hg19: chr17-34147320; API