17-35809864-G-A

Position:

• chr17-35809864-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Moderate BP6_Moderate BA1

The NM_139215.3(TAF15):​c.7+288G>A variant causes a intron change. The variant allele was found at a frequency of 0.0275 in 582,732 control chromosomes in the GnomAD database, including 458 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.021 (67 hom., cov: 32)
  • Exomes 𝑓: 0.030 (391 hom.)
• Consequence: TAF15 NM_139215.3 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 3.87

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BP6: Variant 17-35809864-G-A is Benign according to our data. Variant chr17-35809864-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1218302.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAF15	NM_139215.3	c.7+288G>A		intron_variant		ENST00000605844.6
TAF15	NM_003487.4	c.7+288G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAF15	ENST00000605844.6	c.7+288G>A		intron_variant		1	NM_139215.3	P2

Frequencies

GnomAD3 genomes AF: 0.0213 AC: 3235 AN: 152150 Hom.: 67 Cov.: 32

Gnomad AFR AF: 0.00492

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0120

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0139

Gnomad FIN AF: 0.0361

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0250

Gnomad OTH AF: 0.0172

GnomAD4 exome AF: 0.0298 AC: 12817 AN: 430464 Hom.: 391 Cov.: 0 AF XY: 0.0286 AC XY: 6477 AN XY: 226074

Gnomad4 AFR exome AF: 0.00597

Gnomad4 AMR exome AF: 0.0120

Gnomad4 ASJ exome AF: 0.0152

Gnomad4 EAS exome AF: 0.134

Gnomad4 SAS exome AF: 0.0106

Gnomad4 FIN exome AF: 0.0285

Gnomad4 NFE exome AF: 0.0247

Gnomad4 OTH exome AF: 0.0267

GnomAD4 genome AF: 0.0212 AC: 3232 AN: 152268 Hom.: 67 Cov.: 32 AF XY: 0.0224 AC XY: 1665 AN XY: 74452

Gnomad4 AFR AF: 0.00491

Gnomad4 AMR AF: 0.0120

Gnomad4 ASJ AF: 0.0130

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.0139

Gnomad4 FIN AF: 0.0361

Gnomad4 NFE AF: 0.0250

Gnomad4 OTH AF: 0.0175

Alfa AF: 0.00497 Hom.: 0

Bravo AF: 0.0200

Asia WGS AF: 0.0430 AC: 151 AN: 3478

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 17, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	20
DANN	Uncertain	0.98
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs117281993; hg19: chr17-34136868;