2-192469177-C-T

Variant names:

• chr2-192469177-C-T
• rs1385351

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 0.761 in 151,962 control chromosomes in the GnomAD database, including 44,554 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 0.76 (44554 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.19
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.825 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: 0.761 AC: 115497 AN: 151842 Hom.: 44520 Cov.: 32

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.651

Gnomad NFE AF: 0.831

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.761 AC: 115582 AN: 151962 Hom.: 44554 Cov.: 32 AF XY: 0.761 AC XY: 56530 AN XY: 74252

African (AFR) AF: 0.624 AC: 25884 AN: 41464

American (AMR) AF: 0.780 AC: 11882 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.741 AC: 2570 AN: 3466

East Asian (EAS) AF: 0.778 AC: 4025 AN: 5174

South Asian (SAS) AF: 0.770 AC: 3713 AN: 4822

European-Finnish (FIN) AF: 0.816 AC: 8625 AN: 10574

Middle Eastern (MID) AF: 0.655 AC: 190 AN: 290

European-Non Finnish (NFE) AF: 0.831 AC: 56415 AN: 67914

Other (OTH) AF: 0.727 AC: 1531 AN: 2106

Alfa AF: 0.804 Hom.: 145587

Bravo AF: 0.751

Asia WGS AF: 0.729 AC: 2529 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	12
DANN	Benign	0.44
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs1385351; hg19: chr2-193333903;