2-240348810-C-T

Variant names:

• chr2-240348810-C-T
• rs1320125

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 0.438 in 151,966 control chromosomes in the GnomAD database, including 16,728 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 0.44 (16728 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.576 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: 0.438 AC: 66492 AN: 151846 Hom.: 16733 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.0745

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.438 AC: 66494 AN: 151966 Hom.: 16728 Cov.: 32 AF XY: 0.427 AC XY: 31734 AN XY: 74274

African (AFR) AF: 0.222 AC: 9209 AN: 41440

American (AMR) AF: 0.489 AC: 7464 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1991 AN: 3470

East Asian (EAS) AF: 0.0745 AC: 383 AN: 5144

South Asian (SAS) AF: 0.364 AC: 1755 AN: 4820

European-Finnish (FIN) AF: 0.433 AC: 4577 AN: 10574

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.580 AC: 39429 AN: 67944

Other (OTH) AF: 0.472 AC: 995 AN: 2106

Alfa AF: 0.536 Hom.: 84127

Bravo AF: 0.430

Asia WGS AF: 0.250 AC: 871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.60
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs1320125; hg19: chr2-241288227;