chr2-120365807-T-G

Variant names:

• chr2-120365807-T-G
• rs12711941

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 0.687 in 152,176 control chromosomes in the GnomAD database, including 36,632 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 0.69 (36632 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.82 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: 0.687 AC: 104467 AN: 152056 Hom.: 36599 Cov.: 33

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.687 AC: 104551 AN: 152176 Hom.: 36632 Cov.: 33 AF XY: 0.690 AC XY: 51309 AN XY: 74386

African (AFR) AF: 0.827 AC: 34339 AN: 41516

American (AMR) AF: 0.651 AC: 9962 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2361 AN: 3468

East Asian (EAS) AF: 0.819 AC: 4238 AN: 5174

South Asian (SAS) AF: 0.598 AC: 2887 AN: 4828

European-Finnish (FIN) AF: 0.665 AC: 7050 AN: 10594

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41537 AN: 67986

Other (OTH) AF: 0.682 AC: 1436 AN: 2106

Alfa AF: 0.633 Hom.: 114007

Bravo AF: 0.693

Asia WGS AF: 0.738 AC: 2566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.61
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs12711941; hg19: chr2-121123383;