rs10204426

Variant names:

• chr2-85676785-C-A
• rs10204426

Your query was ambiguous. Multiple possible variants found:

• chr2-85676785-C-A
• chr2-85676785-C-G
• chr2-85676785-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 0.625 in 151,996 control chromosomes in the GnomAD database, including 30,066 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 0.62 (30066 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.707 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: 0.624 AC: 94844 AN: 151878 Hom.: 30035 Cov.: 32

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.625 AC: 94925 AN: 151996 Hom.: 30066 Cov.: 32 AF XY: 0.623 AC XY: 46292 AN XY: 74276

African (AFR) AF: 0.714 AC: 29602 AN: 41468

American (AMR) AF: 0.582 AC: 8893 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 2560 AN: 3470

East Asian (EAS) AF: 0.599 AC: 3096 AN: 5166

South Asian (SAS) AF: 0.699 AC: 3365 AN: 4816

European-Finnish (FIN) AF: 0.510 AC: 5377 AN: 10536

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39861 AN: 67952

Other (OTH) AF: 0.626 AC: 1320 AN: 2110

Alfa AF: 0.608 Hom.: 20692

Bravo AF: 0.635

Asia WGS AF: 0.654 AC: 2272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.52
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs10204426; hg19: chr2-85903908;