17-35822344-CA-C

Position:

• chr17-35822344-CA-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_139215.3(TAF15):​c.291-278delA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.014 (11 hom., cov: 30)
  • Failed GnomAD Quality Control
• Consequence: TAF15 NM_139215.3 intron
• Clinical Significance: Likely 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]

ENSG00000270894 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP6: Variant 17-35822344-CA-C is Benign according to our data. Variant chr17-35822344-CA-C is described in ClinVar as [Likely_benign]. Clinvar id is 1216247.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAF15	NM_139215.3	c.291-278delA		intron_variant		ENST00000605844.6	NP_631961.1
TAF15	NM_003487.4	c.282-278delA		intron_variant			NP_003478.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAF15	ENST00000605844.6	c.291-278delA		intron_variant		1	NM_139215.3	ENSP00000474096.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 941 AN: 67426 Hom.: 11 Cov.: 30 FAILED QC

Gnomad AFR AF: 0.00510

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00841

Gnomad ASJ AF: 0.00332

Gnomad EAS AF: 0.0157

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.0925

Gnomad MID AF: 0.0319

Gnomad NFE AF: 0.00619

Gnomad OTH AF: 0.00468

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0139 AC: 940 AN: 67458 Hom.: 11 Cov.: 30 AF XY: 0.0184 AC XY: 587 AN XY: 31942

Gnomad4 AFR AF: 0.00509

Gnomad4 AMR AF: 0.00840

Gnomad4 ASJ AF: 0.00332

Gnomad4 EAS AF: 0.0157

Gnomad4 SAS AF: 0.0996

Gnomad4 FIN AF: 0.0925

Gnomad4 NFE AF: 0.00619

Gnomad4 OTH AF: 0.00466

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 21, 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;