rs10865531

Variant names:

• chr2-2393451-C-G
• rs10865531

Your query was ambiguous. Multiple possible variants found:

• chr2-2393451-C-G
• chr2-2393451-C-T

Variant summary

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

The variant allele was found at a frequency of 0.982 in 151,840 control chromosomes in the GnomAD database, including 73,190 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 0.98 (73190 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 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

Frequencies

GnomAD3 genomes AF: 0.982 AC: 148918 AN: 151722 Hom.: 73134 Cov.: 29

Gnomad AFR AF: 0.938

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.991

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.999

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.988

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

GnomAD4 genome AF: 0.982 AC: 149033 AN: 151840 Hom.: 73190 Cov.: 29 AF XY: 0.983 AC XY: 72937 AN XY: 74194

African (AFR) AF: 0.938 AC: 38832 AN: 41382

American (AMR) AF: 0.991 AC: 15131 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.999 AC: 3461 AN: 3464

East Asian (EAS) AF: 0.999 AC: 5121 AN: 5124

South Asian (SAS) AF: 0.999 AC: 4795 AN: 4798

European-Finnish (FIN) AF: 0.999 AC: 10548 AN: 10558

Middle Eastern (MID) AF: 0.986 AC: 284 AN: 288

European-Non Finnish (NFE) AF: 0.999 AC: 67868 AN: 67936

Other (OTH) AF: 0.987 AC: 2083 AN: 2110

Alfa AF: 0.998 Hom.: 3321

Bravo AF: 0.981

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
DANN	Benign	0.52
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10865531; hg19: chr2-2397223;