rs4239252

chr17-35836561-G-Achr17-35836561-G-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_139215.3(TAF15):c.783+320G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 152,030 control chromosomes in the GnomAD database, including 9,584 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.31 (9584 hom., cov: 32)
• Consequence: TAF15 NM_139215.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.966

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BP6: Variant 17-35836561-G-A is Benign according to our data. Variant chr17-35836561-G-A is described in ClinVar as [Benign]. Clinvar id is 1242916.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAF15	NM_139215.3	c.783+320G>A		intron_variant		ENST00000605844.6
TAF15	NM_003487.4	c.774+320G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAF15	ENST00000605844.6	c.783+320G>A		intron_variant		1	NM_139215.3	P2

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47335 AN: 151910 Hom.: 9536 Cov.: 32

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.312 AC: 47455 AN: 152030 Hom.: 9584 Cov.: 32 AF XY: 0.313 AC XY: 23237 AN XY: 74320

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.278

Alfa AF: 0.203 Hom.: 2811

Bravo AF: 0.329

Asia WGS AF: 0.427 AC: 1483 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

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	6.2
Dann	Benign	0.23

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: rs4239252; hg19: chr17-34163565;