2-4151151-T-G

Variant names:

• chr2-4151151-T-G
• rs1983365

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 0.612 in 152,032 control chromosomes in the GnomAD database, including 29,011 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 0.61 (29011 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 2 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 (AFR) allele frequency at 95% confidence interval = 0.72 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: 0.612 AC: 92956 AN: 151914 Hom.: 28968 Cov.: 32

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.612 AC: 93058 AN: 152032 Hom.: 29011 Cov.: 32 AF XY: 0.614 AC XY: 45616 AN XY: 74308

African (AFR) AF: 0.727 AC: 30135 AN: 41472

American (AMR) AF: 0.613 AC: 9369 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2078 AN: 3464

East Asian (EAS) AF: 0.577 AC: 2982 AN: 5164

South Asian (SAS) AF: 0.560 AC: 2695 AN: 4816

European-Finnish (FIN) AF: 0.614 AC: 6474 AN: 10542

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37377 AN: 67976

Other (OTH) AF: 0.601 AC: 1266 AN: 2108

Alfa AF: 0.571 Hom.: 18277

Bravo AF: 0.618

Asia WGS AF: 0.615 AC: 2141 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	0.96
DANN	Benign	0.59
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1983365; hg19: chr2-4198741;