rs998358

Variant names:

• chr8-122760713-A-T
• rs998358

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 0.374 in 152,062 control chromosomes in the GnomAD database, including 12,475 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 0.37 (12475 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56793 AN: 151944 Hom.: 12436 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.374 AC: 56881 AN: 152062 Hom.: 12475 Cov.: 32 AF XY: 0.374 AC XY: 27807 AN XY: 74344

African (AFR) AF: 0.601 AC: 24918 AN: 41478

American (AMR) AF: 0.456 AC: 6968 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 553 AN: 3468

East Asian (EAS) AF: 0.312 AC: 1608 AN: 5162

South Asian (SAS) AF: 0.233 AC: 1123 AN: 4820

European-Finnish (FIN) AF: 0.276 AC: 2918 AN: 10586

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17645 AN: 67948

Other (OTH) AF: 0.348 AC: 734 AN: 2110

Alfa AF: 0.319 Hom.: 1148

Bravo AF: 0.401

Asia WGS AF: 0.289 AC: 1003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.81
DANN	Benign	0.70
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs998358; hg19: chr8-123772952;