2-600575-G-T

Variant names:

• chr2-600575-G-T
• rs2683992

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 0.838 in 152,300 control chromosomes in the GnomAD database, including 53,618 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 0.84 (53618 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 10 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 = 0.9 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: 0.838 AC: 127507 AN: 152182 Hom.: 53583 Cov.: 35

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.838 AC: 127596 AN: 152300 Hom.: 53618 Cov.: 35 AF XY: 0.839 AC XY: 62508 AN XY: 74478

African (AFR) AF: 0.867 AC: 36024 AN: 41562

American (AMR) AF: 0.864 AC: 13213 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.721 AC: 2504 AN: 3472

East Asian (EAS) AF: 0.921 AC: 4777 AN: 5184

South Asian (SAS) AF: 0.742 AC: 3580 AN: 4824

European-Finnish (FIN) AF: 0.846 AC: 8987 AN: 10620

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.819 AC: 55747 AN: 68030

Other (OTH) AF: 0.832 AC: 1758 AN: 2114

Alfa AF: 0.825 Hom.: 18926

Bravo AF: 0.844

Asia WGS AF: 0.859 AC: 2989 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.22
DANN	Benign	0.65
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2683992; hg19: chr2-600575;