rs6430764

Positions:

• chr2-137962853-C-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 0.534 in 152,058 control chromosomes in the GnomAD database, including 22,342 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 0.53 (22342 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83

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 (AMR) allele frequency at 95% confidence interval = 0.613 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: 0.534 AC: 81150 AN: 151938 Hom.: 22335 Cov.: 34

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.534 AC: 81190 AN: 152058 Hom.: 22342 Cov.: 34 AF XY: 0.533 AC XY: 39637 AN XY: 74332

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.621

Gnomad4 SAS AF: 0.577

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.594

Gnomad4 OTH AF: 0.523

Alfa AF: 0.569 Hom.: 24073

Bravo AF: 0.538

Asia WGS AF: 0.568 AC: 1975 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.32
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6430764; hg19: chr2-138720423;