rs1424642

Variant names:

• chr2-57069423-A-C
• rs1424642

Your query was ambiguous. Multiple possible variants found:

• chr2-57069423-A-C
• chr2-57069423-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 0.775 in 151,794 control chromosomes in the GnomAD database, including 46,080 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 0.77 (46080 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.878
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 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: 0.775 AC: 117479 AN: 151674 Hom.: 46020 Cov.: 33

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.775 AC: 117607 AN: 151794 Hom.: 46080 Cov.: 33 AF XY: 0.770 AC XY: 57169 AN XY: 74208

African (AFR) AF: 0.844 AC: 35031 AN: 41496

American (AMR) AF: 0.705 AC: 10722 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2605 AN: 3460

East Asian (EAS) AF: 0.460 AC: 2369 AN: 5146

South Asian (SAS) AF: 0.780 AC: 3760 AN: 4820

European-Finnish (FIN) AF: 0.766 AC: 8111 AN: 10594

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.772 AC: 52280 AN: 67762

Other (OTH) AF: 0.781 AC: 1650 AN: 2112

Alfa AF: 0.770 Hom.: 142675

Bravo AF: 0.771

Asia WGS AF: 0.678 AC: 2357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.94
DANN	Benign	0.31
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs1424642; hg19: chr2-57296558;