rs9369425

Variant names:

• chr6-43843237-G-A
• rs9369425
• ENST00000719551.1:n.315+604G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-43843237-G-A
• chr6-43843237-G-T

Variant summary

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

The ENST00000719551.1(ENSG00000283573):​n.315+604G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 152,058 control chromosomes in the GnomAD database, including 34,870 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 0.67 (34870 hom., cov: 32)
• Consequence: ENSG00000283573 ENST00000719551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 14 publications found

Genes affected

ENSG00000283573 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.846 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375070	XR_007059588.1	n.315+604G>A		intron_variant	Intron 2 of 2
LOC105375070	XR_007059589.1	n.315+604G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283573	ENST00000719551.1	n.315+604G>A		intron_variant	Intron 2 of 2
ENSG00000283573	ENST00000719552.1	n.403+604G>A		intron_variant	Intron 2 of 2
ENSG00000283573	ENST00000719558.1	n.198+604G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101732 AN: 151940 Hom.: 34866 Cov.: 32

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.669 AC: 101770 AN: 152058 Hom.: 34870 Cov.: 32 AF XY: 0.672 AC XY: 49965 AN XY: 74350

African (AFR) AF: 0.521 AC: 21595 AN: 41410

American (AMR) AF: 0.760 AC: 11617 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.720 AC: 2500 AN: 3470

East Asian (EAS) AF: 0.867 AC: 4493 AN: 5184

South Asian (SAS) AF: 0.765 AC: 3690 AN: 4826

European-Finnish (FIN) AF: 0.693 AC: 7319 AN: 10562

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.711 AC: 48339 AN: 68002

Other (OTH) AF: 0.665 AC: 1404 AN: 2110

Alfa AF: 0.582 Hom.: 2359

Bravo AF: 0.668

Asia WGS AF: 0.775 AC: 2692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.030
DANN	Benign	0.54
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs9369425; hg19: chr6-43810974; COSMIC: COSV56540787;