rs2848713

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000288587 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0113

Gnomad4 AMR AF: 0.0579

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.0941

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.0658

Gnomad4 NFE AF: 0.0670

Gnomad4 OTH AF: 0.0802

Alfa AF: 0.0527 Hom.: 27

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2848713; hg19: chr6-31384479;