rs2929593

Variant names:

• chr8-73001278-T-C
• rs2929593

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 0.585 in 151,830 control chromosomes in the GnomAD database, including 27,245 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 0.58 (27245 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.479
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.69 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: 0.585 AC: 88732 AN: 151714 Hom.: 27245 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.748

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.585 AC: 88770 AN: 151830 Hom.: 27245 Cov.: 32 AF XY: 0.582 AC XY: 43202 AN XY: 74202

African (AFR) AF: 0.405 AC: 16697 AN: 41250

American (AMR) AF: 0.538 AC: 8220 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2496 AN: 3470

East Asian (EAS) AF: 0.423 AC: 2184 AN: 5168

South Asian (SAS) AF: 0.577 AC: 2784 AN: 4822

European-Finnish (FIN) AF: 0.674 AC: 7107 AN: 10538

Middle Eastern (MID) AF: 0.743 AC: 217 AN: 292

European-Non Finnish (NFE) AF: 0.696 AC: 47300 AN: 67988

Other (OTH) AF: 0.613 AC: 1293 AN: 2110

Alfa AF: 0.639 Hom.: 10824

Bravo AF: 0.567

Asia WGS AF: 0.499 AC: 1734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.4
DANN	Benign	0.61
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs2929593; hg19: chr8-73913513;