rs2741302

Variant names:

• chr2-232363123-A-C
• rs2741302

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 0.815 in 152,062 control chromosomes in the GnomAD database, including 50,844 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 0.81 (50844 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.832 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: 0.815 AC: 123761 AN: 151944 Hom.: 50796 Cov.: 32

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.894

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.898

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.815 AC: 123864 AN: 152062 Hom.: 50844 Cov.: 32 AF XY: 0.810 AC XY: 60209 AN XY: 74312

African (AFR) AF: 0.832 AC: 34550 AN: 41502

American (AMR) AF: 0.782 AC: 11953 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.898 AC: 3119 AN: 3472

East Asian (EAS) AF: 0.492 AC: 2532 AN: 5146

South Asian (SAS) AF: 0.854 AC: 4107 AN: 4808

European-Finnish (FIN) AF: 0.796 AC: 8423 AN: 10580

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.829 AC: 56327 AN: 67954

Other (OTH) AF: 0.836 AC: 1765 AN: 2110

Alfa AF: 0.826 Hom.: 225052

Bravo AF: 0.815

Asia WGS AF: 0.717 AC: 2495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.8
DANN	Benign	0.64
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2741302; hg19: chr2-233227833;