rs2357982

chr2-161029592-C-G

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 0.309 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.246

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.292

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.89
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2357982; hg19: chr2-161886103;