rs4239252

Variant names:

• chr17-35836561-G-A
• rs4239252
• NM_139215.3:c.783+320G>A

Your query was ambiguous. Multiple possible variants found:

• chr17-35836561-G-A
• chr17-35836561-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 19 publications found

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]

TAF15 Gene-Disease associations (from GenCC):

• amyotrophic lateral sclerosis

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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 rank	MANE	Protein	UniProt
TAF15	NM_139215.3	c.783+320G>A		intron_variant	Intron 10 of 15	ENST00000605844.6	NP_631961.1
TAF15	NM_003487.4	c.774+320G>A		intron_variant	Intron 10 of 15		NP_003478.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAF15	ENST00000605844.6	c.783+320G>A		intron_variant	Intron 10 of 15	1	NM_139215.3	ENSP00000474096.1

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

African (AFR) AF: 0.564 AC: 23379 AN: 41456

American (AMR) AF: 0.283 AC: 4314 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 646 AN: 3470

East Asian (EAS) AF: 0.468 AC: 2417 AN: 5162

South Asian (SAS) AF: 0.349 AC: 1681 AN: 4820

European-Finnish (FIN) AF: 0.178 AC: 1875 AN: 10558

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12280 AN: 67988

Other (OTH) AF: 0.278 AC: 588 AN: 2114

Alfa AF: 0.211 Hom.: 3947

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

Jul 03, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.2
DANN	Benign	0.23
PhyloP100		0.97

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

Other links and lift over

dbSNP: rs4239252; hg19: chr17-34163565;