2-42758663-T-C

Variant names:

• chr2-42758663-T-C
• rs6719977

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 0.656 in 152,056 control chromosomes in the GnomAD database, including 33,891 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 0.66 (33891 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 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: 0.656 AC: 99678 AN: 151938 Hom.: 33835 Cov.: 31

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.656 AC: 99796 AN: 152056 Hom.: 33891 Cov.: 31 AF XY: 0.658 AC XY: 48930 AN XY: 74308

African (AFR) AF: 0.820 AC: 34015 AN: 41462

American (AMR) AF: 0.695 AC: 10635 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2190 AN: 3470

East Asian (EAS) AF: 0.802 AC: 4153 AN: 5180

South Asian (SAS) AF: 0.729 AC: 3514 AN: 4818

European-Finnish (FIN) AF: 0.561 AC: 5923 AN: 10562

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37336 AN: 67960

Other (OTH) AF: 0.657 AC: 1387 AN: 2110

Alfa AF: 0.569 Hom.: 28187

Bravo AF: 0.674

Asia WGS AF: 0.794 AC: 2759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	8.4
DANN	Benign	0.80
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs6719977; hg19: chr2-42985803;