rs2848713

Variant names:

• chr6-31416702-G-A
• rs2848713
• ENST00000673857.1:n.62+15939G>A

Variant summary

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

The ENST00000673857.1(ENSG00000288587):​n.62+15939G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.056 in 152,082 control chromosomes in the GnomAD database, including 421 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 0.056 (421 hom., cov: 33)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.782
• Publications: 26 publications found

Genes affected

ENSG00000288587 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288587	ENST00000673857.1	n.62+15939G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0560 AC: 8510 AN: 151964 Hom.: 420 Cov.: 33

Gnomad AFR AF: 0.0113

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0580

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0937

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.0658

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0669

Gnomad OTH AF: 0.0815

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

GnomAD4 genome AF: 0.0560 AC: 8513 AN: 152082 Hom.: 421 Cov.: 33 AF XY: 0.0586 AC XY: 4360 AN XY: 74366

African (AFR) AF: 0.0113 AC: 468 AN: 41460

American (AMR) AF: 0.0579 AC: 882 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 358 AN: 3466

East Asian (EAS) AF: 0.0941 AC: 486 AN: 5166

South Asian (SAS) AF: 0.172 AC: 829 AN: 4822

European-Finnish (FIN) AF: 0.0658 AC: 698 AN: 10600

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0670 AC: 4555 AN: 68016

Other (OTH) AF: 0.0802 AC: 169 AN: 2108

Alfa AF: 0.0656 Hom.: 1293

Bravo AF: 0.0513

Asia WGS AF: 0.102 AC: 354 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.98
DANN	Benign	0.75
PhyloP100		-0.78
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: rs2848713; hg19: chr6-31384479;