rs4341893

Variant names:

• chr2-20935817-A-G
• rs4341893

Your query was ambiguous. Multiple possible variants found:

• chr2-20935817-A-G
• chr2-20935817-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 0.722 in 152,042 control chromosomes in the GnomAD database, including 40,113 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 0.72 (40113 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 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: 0.722 AC: 109719 AN: 151924 Hom.: 40064 Cov.: 31

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.722 AC: 109826 AN: 152042 Hom.: 40113 Cov.: 31 AF XY: 0.720 AC XY: 53492 AN XY: 74302

African (AFR) AF: 0.837 AC: 34704 AN: 41478

American (AMR) AF: 0.700 AC: 10686 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.762 AC: 2644 AN: 3470

East Asian (EAS) AF: 0.732 AC: 3788 AN: 5174

South Asian (SAS) AF: 0.662 AC: 3184 AN: 4812

European-Finnish (FIN) AF: 0.658 AC: 6943 AN: 10544

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.671 AC: 45589 AN: 67982

Other (OTH) AF: 0.767 AC: 1618 AN: 2110

Alfa AF: 0.691 Hom.: 158171

Bravo AF: 0.730

Asia WGS AF: 0.716 AC: 2490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.7
DANN	Benign	0.23
PhyloP100		0.079

Splicing

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

Other links and lift over

dbSNP: rs4341893; hg19: chr2-21135577;