rs2357982

Variant names:

• chr2-161029592-C-G
• rs2357982

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 0.309 in 151,874 control chromosomes in the GnomAD database, including 7,382 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 0.31 (7382 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.839
• Publications: 7 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 (AFR) allele frequency at 95% confidence interval = 0.331 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: 0.309 AC: 46850 AN: 151758 Hom.: 7344 Cov.: 31

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.309 AC: 46938 AN: 151874 Hom.: 7382 Cov.: 31 AF XY: 0.311 AC XY: 23096 AN XY: 74218

African (AFR) AF: 0.335 AC: 13885 AN: 41400

American (AMR) AF: 0.237 AC: 3620 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 856 AN: 3470

East Asian (EAS) AF: 0.246 AC: 1265 AN: 5152

South Asian (SAS) AF: 0.269 AC: 1297 AN: 4816

European-Finnish (FIN) AF: 0.395 AC: 4156 AN: 10512

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20834 AN: 67936

Other (OTH) AF: 0.292 AC: 618 AN: 2114

Alfa AF: 0.314 Hom.: 925

Bravo AF: 0.295

Asia WGS AF: 0.298 AC: 1036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.89
DANN	Benign	0.39
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs2357982; hg19: chr2-161886103;