rs3923037

Variant names:

• chr2-20948514-A-C
• rs3923037

Your query was ambiguous. Multiple possible variants found:

• chr2-20948514-A-C
• chr2-20948514-A-G
• chr2-20948514-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 0.419 in 152,102 control chromosomes in the GnomAD database, including 14,131 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 (14131 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.828 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: 0.419 AC: 63664 AN: 151984 Hom.: 14125 Cov.: 33

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.419 AC: 63702 AN: 152102 Hom.: 14131 Cov.: 33 AF XY: 0.423 AC XY: 31480 AN XY: 74360

African (AFR) AF: 0.462 AC: 19153 AN: 41464

American (AMR) AF: 0.386 AC: 5911 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1497 AN: 3470

East Asian (EAS) AF: 0.849 AC: 4402 AN: 5186

South Asian (SAS) AF: 0.597 AC: 2871 AN: 4812

European-Finnish (FIN) AF: 0.370 AC: 3913 AN: 10580

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.360 AC: 24481 AN: 67976

Other (OTH) AF: 0.425 AC: 899 AN: 2114

Alfa AF: 0.358 Hom.: 4837

Bravo AF: 0.420

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.65
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs3923037; hg19: chr2-21148274;