17-35820529-CT-C

Position:

• chr17-35820529-CT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_139215.3(TAF15):​c.290+105delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 821,506 control chromosomes in the GnomAD database, including 295 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.036 (260 hom., cov: 32)
  • Exomes 𝑓: 0.18 (35 hom.)
• Consequence: TAF15 NM_139215.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0250

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]

ENSG00000270894 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 17-35820529-CT-C is Benign according to our data. Variant chr17-35820529-CT-C is described in ClinVar as [Benign]. Clinvar id is 1265877.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAF15	NM_139215.3	c.290+105delT		intron_variant		ENST00000605844.6	NP_631961.1
TAF15	NM_003487.4	c.281+105delT		intron_variant			NP_003478.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAF15	ENST00000605844.6	c.290+105delT		intron_variant		1	NM_139215.3	ENSP00000474096.1

Frequencies

GnomAD3 genomes AF: 0.0356 AC: 5110 AN: 143564 Hom.: 260 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0148

Gnomad ASJ AF: 0.00688

Gnomad EAS AF: 0.00260

Gnomad SAS AF: 0.00110

Gnomad FIN AF: 0.00959

Gnomad MID AF: 0.0268

Gnomad NFE AF: 0.00276

Gnomad OTH AF: 0.0262

GnomAD4 exome AF: 0.177 AC: 119759 AN: 677890 Hom.: 35 AF XY: 0.181 AC XY: 61652 AN XY: 339838

Gnomad4 AFR exome AF: 0.268

Gnomad4 AMR exome AF: 0.254

Gnomad4 ASJ exome AF: 0.229

Gnomad4 EAS exome AF: 0.260

Gnomad4 SAS exome AF: 0.232

Gnomad4 FIN exome AF: 0.203

Gnomad4 NFE exome AF: 0.160

Gnomad4 OTH exome AF: 0.201

GnomAD4 genome AF: 0.0357 AC: 5120 AN: 143616 Hom.: 260 Cov.: 32 AF XY: 0.0342 AC XY: 2385 AN XY: 69714

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.0148

Gnomad4 ASJ AF: 0.00688

Gnomad4 EAS AF: 0.00261

Gnomad4 SAS AF: 0.00110

Gnomad4 FIN AF: 0.00959

Gnomad4 NFE AF: 0.00276

Gnomad4 OTH AF: 0.0260

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 02, 2019

- -

Computational scores

Source: dbNSFP v4.3

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: rs879823976; hg19: chr17-34147533;