2-41906292-C-T

Variant names:

• chr2-41906292-C-T
• rs2374341

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 0.324 in 151,964 control chromosomes in the GnomAD database, including 8,300 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 0.32 (8300 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.418 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: 0.324 AC: 49176 AN: 151846 Hom.: 8298 Cov.: 31

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.324 AC: 49214 AN: 151964 Hom.: 8300 Cov.: 31 AF XY: 0.329 AC XY: 24425 AN XY: 74264

African (AFR) AF: 0.232 AC: 9629 AN: 41446

American (AMR) AF: 0.325 AC: 4961 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1284 AN: 3468

East Asian (EAS) AF: 0.341 AC: 1759 AN: 5156

South Asian (SAS) AF: 0.433 AC: 2086 AN: 4814

European-Finnish (FIN) AF: 0.401 AC: 4237 AN: 10554

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24094 AN: 67934

Other (OTH) AF: 0.336 AC: 708 AN: 2106

Alfa AF: 0.337 Hom.: 23793

Bravo AF: 0.309

Asia WGS AF: 0.440 AC: 1525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.52
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs2374341; hg19: chr2-42133432;