rs887956

Variant names:

• chr2-58370822-A-C
• rs887956

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 0.157 in 152,166 control chromosomes in the GnomAD database, including 2,103 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 0.16 (2103 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.520

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 (EAS) allele frequency at 95% confidence interval = 0.302 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: 0.157 AC: 23897 AN: 152046 Hom.: 2104 Cov.: 32

Gnomad AFR AF: 0.0873

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.157 AC: 23907 AN: 152166 Hom.: 2103 Cov.: 32 AF XY: 0.158 AC XY: 11767 AN XY: 74376

Gnomad4 AFR AF: 0.0875

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.188

Alfa AF: 0.169 Hom.: 2289

Bravo AF: 0.159

Asia WGS AF: 0.276 AC: 955 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	11
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs887956; hg19: chr2-58597957;