rs594544

Variant names:

• chr9-21372124-G-A
• rs594544

Your query was ambiguous. Multiple possible variants found:

• chr9-21372124-G-A
• chr9-21372124-G-C
• chr9-21372124-G-T

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 0.387 in 152,002 control chromosomes in the GnomAD database, including 12,554 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 0.39 (12554 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.626 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: 0.387 AC: 58723 AN: 151884 Hom.: 12530 Cov.: 31

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.387 AC: 58799 AN: 152002 Hom.: 12554 Cov.: 31 AF XY: 0.389 AC XY: 28921 AN XY: 74258

Gnomad4 AFR AF: 0.545

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.644

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.352

Alfa AF: 0.327 Hom.: 3359

Bravo AF: 0.401

Asia WGS AF: 0.494 AC: 1719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs594544; hg19: chr9-21372123;