rs2596438

Variant names:

• chr6-31372094-G-A
• rs2596438
• ENST00000649421.2:n.275-2789G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-31372094-G-A
• chr6-31372094-G-C
• chr6-31372094-G-T

Variant summary

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

The ENST00000649421.2(ENSG00000285647):​n.275-2789G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.848 in 151,244 control chromosomes in the GnomAD database, including 54,811 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 0.85 (54811 hom., cov: 33)
• Consequence: ENSG00000285647 ENST00000649421.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 10 publications found

Genes affected

ENSG00000285647 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.925 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
ENSG00000285647	ENST00000649421.2	n.275-2789G>A		intron_variant	Intron 1 of 1
ENSG00000298426	ENST00000755446.1	n.327-9886G>A		intron_variant	Intron 1 of 1
ENSG00000285647	ENST00000755530.1	n.203-2789G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.848 AC: 128188 AN: 151130 Hom.: 54759 Cov.: 33

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.895

Gnomad ASJ AF: 0.931

Gnomad EAS AF: 0.948

Gnomad SAS AF: 0.932

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.879

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

GnomAD4 genome AF: 0.848 AC: 128295 AN: 151244 Hom.: 54811 Cov.: 33 AF XY: 0.852 AC XY: 62854 AN XY: 73806

African (AFR) AF: 0.837 AC: 34695 AN: 41458

American (AMR) AF: 0.896 AC: 13391 AN: 14950

Ashkenazi Jewish (ASJ) AF: 0.931 AC: 3231 AN: 3472

East Asian (EAS) AF: 0.948 AC: 4839 AN: 5106

South Asian (SAS) AF: 0.933 AC: 4342 AN: 4654

European-Finnish (FIN) AF: 0.836 AC: 8763 AN: 10476

Middle Eastern (MID) AF: 0.918 AC: 268 AN: 292

European-Non Finnish (NFE) AF: 0.827 AC: 56086 AN: 67838

Other (OTH) AF: 0.882 AC: 1841 AN: 2088

Alfa AF: 0.851 Hom.: 31422

Bravo AF: 0.851

Asia WGS AF: 0.925 AC: 3149 AN: 3404

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.36
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs2596438; hg19: chr6-31339871;