2-67737946-G-C

Variant names:

• chr2-67737946-G-C
• rs1430763

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 0.755 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.675 AC: 27990 AN: 41482

American (AMR) AF: 0.830 AC: 12696 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.846 AC: 2938 AN: 3472

East Asian (EAS) AF: 0.848 AC: 4390 AN: 5176

South Asian (SAS) AF: 0.799 AC: 3851 AN: 4820

European-Finnish (FIN) AF: 0.792 AC: 8395 AN: 10594

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.764 AC: 51933 AN: 67994

Other (OTH) AF: 0.780 AC: 1648 AN: 2114

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
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1430763; hg19: chr2-67965078;