2-4751508-A-G

Variant names:

• chr2-4751508-A-G
• rs1374122

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 0.932 in 152,218 control chromosomes in the GnomAD database, including 66,740 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 0.93 (66740 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.738
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.988 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: 0.932 AC: 141695 AN: 152100 Hom.: 66695 Cov.: 32

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.965

Gnomad ASJ AF: 0.943

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.998

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.994

Gnomad OTH AF: 0.934

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

GnomAD4 genome AF: 0.932 AC: 141799 AN: 152218 Hom.: 66740 Cov.: 32 AF XY: 0.934 AC XY: 69475 AN XY: 74418

African (AFR) AF: 0.780 AC: 32370 AN: 41486

American (AMR) AF: 0.965 AC: 14748 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.943 AC: 3273 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5163 AN: 5164

South Asian (SAS) AF: 0.998 AC: 4814 AN: 4824

European-Finnish (FIN) AF: 1.00 AC: 10625 AN: 10628

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.994 AC: 67646 AN: 68034

Other (OTH) AF: 0.935 AC: 1976 AN: 2114

Alfa AF: 0.950 Hom.: 17461

Bravo AF: 0.922

Asia WGS AF: 0.987 AC: 3432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	8.6
DANN	Benign	0.73
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs1374122; hg19: chr2-4799098;