rs2182241

Variant names:

• chr1-62339468-G-C
• rs2182241

Your query was ambiguous. Multiple possible variants found:

• chr1-62339468-G-C
• chr1-62339468-G-T

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 0.461 in 151,888 control chromosomes in the GnomAD database, including 16,292 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 0.46 (16292 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 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: 0.460 AC: 69885 AN: 151770 Hom.: 16274 Cov.: 31

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.461 AC: 69949 AN: 151888 Hom.: 16292 Cov.: 31 AF XY: 0.459 AC XY: 34097 AN XY: 74218

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.452

Alfa AF: 0.451 Hom.: 2187

Bravo AF: 0.466

Asia WGS AF: 0.520 AC: 1810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.46
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2182241; hg19: chr1-62805139;