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 rank MANE Protein UniProt
TAF15NM_139215.3 linkc.185-16C>T intron_variant Intron 4 of 15 ENST00000605844.6 NP_631961.1 Q92804-1
TAF15NM_003487.4 linkc.176-16C>T intron_variant Intron 4 of 15 NP_003478.1 Q92804-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TAF15ENST00000605844.6 linkc.185-16C>T intron_variant Intron 4 of 15 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
Nov 05, 2020
GeneDx
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

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