rs2842026

Variant names:

• chr1-163063299-A-C
• rs2842026

Your query was ambiguous. Multiple possible variants found:

• chr1-163063299-A-C
• chr1-163063299-A-G
• chr1-163063299-A-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 0.417 in 151,932 control chromosomes in the GnomAD database, including 14,248 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 0.42 (14248 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.938
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 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: 0.418 AC: 63405 AN: 151812 Hom.: 14258 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.417 AC: 63401 AN: 151932 Hom.: 14248 Cov.: 32 AF XY: 0.417 AC XY: 30971 AN XY: 74246

African (AFR) AF: 0.239 AC: 9899 AN: 41448

American (AMR) AF: 0.478 AC: 7280 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1591 AN: 3464

East Asian (EAS) AF: 0.496 AC: 2551 AN: 5148

South Asian (SAS) AF: 0.327 AC: 1575 AN: 4816

European-Finnish (FIN) AF: 0.534 AC: 5648 AN: 10568

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.492 AC: 33424 AN: 67930

Other (OTH) AF: 0.411 AC: 868 AN: 2112

Alfa AF: 0.303 Hom.: 814

Bravo AF: 0.413

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.8
DANN	Benign	0.81
PhyloP100		0.94

Splicing

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

Other links and lift over

dbSNP: rs2842026; hg19: chr1-163033089;