chr2-67746755-T-G

Variant names:

• chr2-67746755-T-G
• rs13432159

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 0.081 in 152,280 control chromosomes in the GnomAD database, including 560 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 0.081 (560 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0810 AC: 12324 AN: 152162 Hom.: 558 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0553

Gnomad ASJ AF: 0.0464

Gnomad EAS AF: 0.0450

Gnomad SAS AF: 0.0339

Gnomad FIN AF: 0.0755

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0805

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0810 AC: 12340 AN: 152280 Hom.: 560 Cov.: 32 AF XY: 0.0795 AC XY: 5922 AN XY: 74476

African (AFR) AF: 0.107 AC: 4466 AN: 41558

American (AMR) AF: 0.0552 AC: 844 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0464 AC: 161 AN: 3472

East Asian (EAS) AF: 0.0451 AC: 234 AN: 5186

South Asian (SAS) AF: 0.0338 AC: 163 AN: 4828

European-Finnish (FIN) AF: 0.0755 AC: 802 AN: 10616

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0804 AC: 5470 AN: 68006

Other (OTH) AF: 0.0681 AC: 144 AN: 2116

Alfa AF: 0.0764 Hom.: 1611

Bravo AF: 0.0797

Asia WGS AF: 0.0440 AC: 155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.026
DANN	Benign	0.66
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs13432159; hg19: chr2-67973887;