rs1873933

chr8-27559905-G-A

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 0.418 in 152,062 control chromosomes in the GnomAD database, including 14,635 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 0.42 (14635 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.359

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.53 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: 0.418 AC: 63518 AN: 151946 Hom.: 14616 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.418 AC: 63569 AN: 152062 Hom.: 14635 Cov.: 32 AF XY: 0.419 AC XY: 31139 AN XY: 74322

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.540

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.405

Alfa AF: 0.483 Hom.: 24106

Bravo AF: 0.407

Asia WGS AF: 0.340 AC: 1182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	4.4
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1873933; hg19: chr8-27417422;