2-67737946-G-C

Variant names:

• chr2-67737946-G-C
• rs1430763

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 0.755 in 152,158 control chromosomes in the GnomAD database, including 43,549 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 0.75 (43549 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.827 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: 0.755 AC: 114762 AN: 152038 Hom.: 43512 Cov.: 32

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.755 AC: 114861 AN: 152158 Hom.: 43549 Cov.: 32 AF XY: 0.758 AC XY: 56392 AN XY: 74382

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.830

Gnomad4 ASJ AF: 0.846

Gnomad4 EAS AF: 0.848

Gnomad4 SAS AF: 0.799

Gnomad4 FIN AF: 0.792

Gnomad4 NFE AF: 0.764

Gnomad4 OTH AF: 0.780

Alfa AF: 0.683 Hom.: 2020

Bravo AF: 0.755

Asia WGS AF: 0.828 AC: 2878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.012
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1430763; hg19: chr2-67965078;