rs998358

chr8-122760713-A-T

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 0.374 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.374 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

Gnomad4 AFR AF: 0.601

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.348

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.81
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs998358; hg19: chr8-123772952;