2-232411009-T-C

Variant names:

• chr2-232411009-T-C
• rs2697781

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 0.692 in 150,910 control chromosomes in the GnomAD database, including 36,338 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 (36338 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.693 AC: 104430 AN: 150794 Hom.: 36316 Cov.: 27

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.756

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.692 AC: 104504 AN: 150910 Hom.: 36338 Cov.: 27 AF XY: 0.695 AC XY: 51182 AN XY: 73678

African (AFR) AF: 0.630 AC: 25803 AN: 40930

American (AMR) AF: 0.689 AC: 10446 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2757 AN: 3464

East Asian (EAS) AF: 0.892 AC: 4515 AN: 5060

South Asian (SAS) AF: 0.687 AC: 3270 AN: 4758

European-Finnish (FIN) AF: 0.733 AC: 7655 AN: 10440

Middle Eastern (MID) AF: 0.776 AC: 225 AN: 290

European-Non Finnish (NFE) AF: 0.703 AC: 47667 AN: 67812

Other (OTH) AF: 0.709 AC: 1480 AN: 2088

Alfa AF: 0.696 Hom.: 11130

Bravo AF: 0.688

Asia WGS AF: 0.798 AC: 2773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.36
DANN	Benign	0.87
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs2697781; hg19: chr2-233275719;