rs337572

Variant names:

• chr9-98724363-G-A
• rs337572

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 0.738 in 152,108 control chromosomes in the GnomAD database, including 41,519 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 0.74 (41519 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.65

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.757 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: 0.738 AC: 112183 AN: 151990 Hom.: 41497 Cov.: 32

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.760

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

GnomAD4 genome AF: 0.738 AC: 112246 AN: 152108 Hom.: 41519 Cov.: 32 AF XY: 0.733 AC XY: 54521 AN XY: 74348

Gnomad4 AFR AF: 0.725

Gnomad4 AMR AF: 0.758

Gnomad4 ASJ AF: 0.791

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.659

Gnomad4 NFE AF: 0.762

Gnomad4 OTH AF: 0.758

Alfa AF: 0.746 Hom.: 5265

Bravo AF: 0.743

Asia WGS AF: 0.633 AC: 2202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0020
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs337572; hg19: chr9-101486645;