chr2-240348810-C-T

Variant names:

• chr2-240348810-C-T
• rs1320125

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.0745

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.580

Gnomad4 OTH AF: 0.472

Alfa AF: 0.558 Hom.: 36727

Bravo AF: 0.430

Asia WGS AF: 0.250 AC: 871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1320125; hg19: chr2-241288227;