chr2-600575-G-T

Position:

• chr2-600575-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.867

Gnomad4 AMR AF: 0.864

Gnomad4 ASJ AF: 0.721

Gnomad4 EAS AF: 0.921

Gnomad4 SAS AF: 0.742

Gnomad4 FIN AF: 0.846

Gnomad4 NFE AF: 0.819

Gnomad4 OTH AF: 0.832

Alfa AF: 0.821 Hom.: 10049

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2683992; hg19: chr2-600575;