rs9521372

chr13-109440697-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 0.0975 in 152,150 control chromosomes in the GnomAD database, including 900 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 0.097 (900 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.345

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 = 0.13 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: 0.0975 AC: 14830 AN: 152032 Hom.: 899 Cov.: 32

Gnomad AFR AF: 0.0247

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.0767

Gnomad SAS AF: 0.0933

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.0975 AC: 14832 AN: 152150 Hom.: 900 Cov.: 32 AF XY: 0.0975 AC XY: 7250 AN XY: 74380

Gnomad4 AFR AF: 0.0246

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.0764

Gnomad4 SAS AF: 0.0942

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.104

Alfa AF: 0.123 Hom.: 311

Bravo AF: 0.0955

Asia WGS AF: 0.0890 AC: 311 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	0.91
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9521372; hg19: chr13-110093044;