rs958660

Variant names:

• chr8-2212161-G-A
• rs958660

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 0.063 in 151,852 control chromosomes in the GnomAD database, including 504 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 0.063 (504 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.581

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 (NFE) allele frequency at 95% confidence interval = 0.0973 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: 0.0631 AC: 9567 AN: 151734 Hom.: 503 Cov.: 32

Gnomad AFR AF: 0.0185

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.0542

Gnomad ASJ AF: 0.0728

Gnomad EAS AF: 0.000585

Gnomad SAS AF: 0.0472

Gnomad FIN AF: 0.0411

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0993

Gnomad OTH AF: 0.0728

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

GnomAD4 genome AF: 0.0630 AC: 9569 AN: 151852 Hom.: 504 Cov.: 32 AF XY: 0.0593 AC XY: 4398 AN XY: 74134

Gnomad4 AFR AF: 0.0184

Gnomad4 AMR AF: 0.0542

Gnomad4 ASJ AF: 0.0728

Gnomad4 EAS AF: 0.000586

Gnomad4 SAS AF: 0.0479

Gnomad4 FIN AF: 0.0411

Gnomad4 NFE AF: 0.0993

Gnomad4 OTH AF: 0.0725

Alfa AF: 0.0786 Hom.: 90

Bravo AF: 0.0628

Asia WGS AF: 0.0270 AC: 95 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs958660; hg19: chr8-2159828;