17-35821079-G-A

Position:

• chr17-35821079-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_139215.3(TAF15):​c.290+642G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0531 in 152,204 control chromosomes in the GnomAD database, including 349 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.053 (349 hom., cov: 32)
• Consequence: TAF15 NM_139215.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.420

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAF15	NM_139215.3	c.290+642G>A		intron_variant		ENST00000605844.6
TAF15	NM_003487.4	c.281+642G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAF15	ENST00000605844.6	c.290+642G>A		intron_variant		1	NM_139215.3	P2
	ENST00000603678.1	n.316+2365G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000603981.1	n.264-4138C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0531 AC: 8073 AN: 152086 Hom.: 347 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0237

Gnomad ASJ AF: 0.0138

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.0149

Gnomad FIN AF: 0.0357

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0254

Gnomad OTH AF: 0.0392

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0531 AC: 8084 AN: 152204 Hom.: 349 Cov.: 32 AF XY: 0.0525 AC XY: 3906 AN XY: 74436

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.0237

Gnomad4 ASJ AF: 0.0138

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.0149

Gnomad4 FIN AF: 0.0357

Gnomad4 NFE AF: 0.0254

Gnomad4 OTH AF: 0.0416

Alfa AF: 0.0275 Hom.: 100

Bravo AF: 0.0567

Asia WGS AF: 0.0510 AC: 179 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.66

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

Other links and lift over

dbSNP: rs4251739; hg19: chr17-34148083;