2-107062032-G-T

Variant names:

• chr2-107062032-G-T
• rs1357692

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 0.672 in 150,928 control chromosomes in the GnomAD database, including 34,274 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 0.67 (34274 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.672 AC: 101297 AN: 150820 Hom.: 34260 Cov.: 28

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.672 AC: 101350 AN: 150928 Hom.: 34274 Cov.: 28 AF XY: 0.679 AC XY: 50001 AN XY: 73668

African (AFR) AF: 0.627 AC: 25761 AN: 41074

American (AMR) AF: 0.653 AC: 9909 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2494 AN: 3468

East Asian (EAS) AF: 0.696 AC: 3578 AN: 5140

South Asian (SAS) AF: 0.784 AC: 3731 AN: 4756

European-Finnish (FIN) AF: 0.781 AC: 7946 AN: 10178

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.674 AC: 45696 AN: 67844

Other (OTH) AF: 0.661 AC: 1381 AN: 2088

Alfa AF: 0.672 Hom.: 61678

Bravo AF: 0.660

Asia WGS AF: 0.729 AC: 2527 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.71
DANN	Benign	0.54
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs1357692; hg19: chr2-107678488;