rs1974435

Variant names:

• chr17-63916736-G-A
• rs1974435
• ENST00000791137.1:n.266-724G>A

Your query was ambiguous. Multiple possible variants found:

• chr17-63916736-G-A
• chr17-63916736-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000791137.1(ENSG00000303015):​n.266-724G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 151,896 control chromosomes in the GnomAD database, including 10,337 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.36 (10337 hom., cov: 31)
• Consequence: ENSG00000303015 ENST00000791137.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390
• Publications: 4 publications found

Genes affected

ENSG00000303015 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268204	XR_002958148.2	n.341-861G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303015	ENST00000791137.1	n.266-724G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54894 AN: 151776 Hom.: 10329 Cov.: 31

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.362 AC: 54937 AN: 151896 Hom.: 10337 Cov.: 31 AF XY: 0.359 AC XY: 26612 AN XY: 74224

African (AFR) AF: 0.256 AC: 10626 AN: 41440

American (AMR) AF: 0.371 AC: 5662 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1527 AN: 3470

East Asian (EAS) AF: 0.408 AC: 2105 AN: 5162

South Asian (SAS) AF: 0.267 AC: 1287 AN: 4812

European-Finnish (FIN) AF: 0.407 AC: 4281 AN: 10518

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28051 AN: 67938

Other (OTH) AF: 0.391 AC: 822 AN: 2100

Alfa AF: 0.386 Hom.: 1443

Bravo AF: 0.359

Asia WGS AF: 0.345 AC: 1201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.37
PhyloP100		-0.039
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1974435; hg19: chr17-61994096; COSMIC: COSV107391263; COSMIC: COSV107391263;