17-35822498-A-G

Variant summary

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

The NM_139215.3(TAF15):c.291-142A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0705 in 723,474 control chromosomes in the GnomAD database, including 3,188 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.10 (1399 hom., cov: 32)
  • Exomes 𝑓: 0.061 (1789 hom.)
• Consequence: TAF15 NM_139215.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.921

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 17-35822498-A-G is Benign according to our data. Variant chr17-35822498-A-G is described in ClinVar as [Benign]. Clinvar id is 1234576.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAF15	NM_139215.3	c.291-142A>G		intron_variant		ENST00000605844.6
TAF15	NM_003487.4	c.282-142A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAF15	ENST00000605844.6	c.291-142A>G		intron_variant		1	NM_139215.3	P2
	ENST00000603678.1	n.317-1111A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000603981.1	n.264-5557T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15929 AN: 152114 Hom.: 1382 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0557

Gnomad ASJ AF: 0.0207

Gnomad EAS AF: 0.0123

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0304

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0529

Gnomad OTH AF: 0.0831

GnomAD4 exome AF: 0.0613 AC: 35040 AN: 571242 Hom.: 1789 AF XY: 0.0643 AC XY: 19318 AN XY: 300432

Gnomad4 AFR exome AF: 0.248

Gnomad4 AMR exome AF: 0.0349

Gnomad4 ASJ exome AF: 0.0255

Gnomad4 EAS exome AF: 0.00784

Gnomad4 SAS exome AF: 0.148

Gnomad4 FIN exome AF: 0.0361

Gnomad4 NFE exome AF: 0.0518

Gnomad4 OTH exome AF: 0.0630

GnomAD4 genome AF: 0.105 AC: 15982 AN: 152232 Hom.: 1399 Cov.: 32 AF XY: 0.104 AC XY: 7756 AN XY: 74430

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.0555

Gnomad4 ASJ AF: 0.0207

Gnomad4 EAS AF: 0.0123

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.0304

Gnomad4 NFE AF: 0.0529

Gnomad4 OTH AF: 0.0822

Alfa AF: 0.0273 Hom.: 19

Bravo AF: 0.109

Asia WGS AF: 0.110 AC: 381 AN: 3478

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

Jul 03, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	14
Dann	Benign	0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.27		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.27		Position offset: -1

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4251744; hg19: chr17-34149502;