17-35822344-C-CA

Variant summary

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

The NM_139215.3(TAF15):c.291-278dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 67,276 control chromosomes in the GnomAD database, including 527 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.11 (527 hom., cov: 30)
• Consequence: TAF15 NM_139215.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.131

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 -10 ACMG points.

• BP6: Variant 17-35822344-C-CA is Benign according to our data. Variant chr17-35822344-C-CA is described in ClinVar as [Benign]. Clinvar id is 1183315.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAF15	NM_139215.3	c.291-278dup		intron_variant		ENST00000605844.6
TAF15	NM_003487.4	c.282-278dup		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAF15	ENST00000605844.6	c.291-278dup		intron_variant		1	NM_139215.3	P2
	ENST00000603678.1	n.317-1247dup		intron_variant, non_coding_transcript_variant		5
	ENST00000603981.1	n.264-5404_264-5403insT		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.108 AC: 7244 AN: 67244 Hom.: 523 Cov.: 30

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0120

Gnomad EAS AF: 0.0640

Gnomad SAS AF: 0.00916

Gnomad FIN AF: 0.0249

Gnomad MID AF: 0.0851

Gnomad NFE AF: 0.0155

Gnomad OTH AF: 0.0972

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

GnomAD4 genome AF: 0.108 AC: 7266 AN: 67276 Hom.: 527 Cov.: 30 AF XY: 0.108 AC XY: 3439 AN XY: 31876

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0120

Gnomad4 EAS AF: 0.0634

Gnomad4 SAS AF: 0.00915

Gnomad4 FIN AF: 0.0249

Gnomad4 NFE AF: 0.0155

Gnomad4 OTH AF: 0.0979

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

Aug 26, 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: rs909362495; hg19: chr17-34149348;