rs576594

Variant names:

• chr9-95556929-A-G
• rs576594

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 0.67 in 152,112 control chromosomes in the GnomAD database, including 35,054 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 0.67 (35054 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.827 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: 0.670 AC: 101855 AN: 151994 Hom.: 34985 Cov.: 32

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.670 AC: 101986 AN: 152112 Hom.: 35054 Cov.: 32 AF XY: 0.672 AC XY: 49957 AN XY: 74346

Gnomad4 AFR AF: 0.834

Gnomad4 AMR AF: 0.643

Gnomad4 ASJ AF: 0.604

Gnomad4 EAS AF: 0.680

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.642

Alfa AF: 0.594 Hom.: 54772

Bravo AF: 0.676

Asia WGS AF: 0.694 AC: 2411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	7.3
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs576594; hg19: chr9-98319211;