rs2929593

chr8-73001278-T-C

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 0.585 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.405

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.719

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.577

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.613

Alfa AF: 0.645 Hom.: 8395

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2929593; hg19: chr8-73913513;