rs1873933

Variant names:

• chr8-27559905-G-A
• rs1873933

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 0.418 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.238 AC: 9868 AN: 41494

American (AMR) AF: 0.540 AC: 8258 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1348 AN: 3472

East Asian (EAS) AF: 0.171 AC: 884 AN: 5162

South Asian (SAS) AF: 0.410 AC: 1975 AN: 4814

European-Finnish (FIN) AF: 0.526 AC: 5570 AN: 10582

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.503 AC: 34179 AN: 67940

Other (OTH) AF: 0.405 AC: 854 AN: 2108

Alfa AF: 0.475 Hom.: 29853

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
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs1873933; hg19: chr8-27417422;