13-109373289-T-G

Variant names:

• chr13-109373289-T-G
• rs9521337

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 0.768 in 152,054 control chromosomes in the GnomAD database, including 46,905 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 0.77 (46905 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.768 AC: 116677 AN: 151936 Hom.: 46881 Cov.: 31

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.807

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.881

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.768 AC: 116748 AN: 152054 Hom.: 46905 Cov.: 31 AF XY: 0.772 AC XY: 57361 AN XY: 74328

Gnomad4 AFR AF: 0.501

Gnomad4 AMR AF: 0.849

Gnomad4 ASJ AF: 0.807

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.828

Gnomad4 FIN AF: 0.881

Gnomad4 NFE AF: 0.867

Gnomad4 OTH AF: 0.787

Alfa AF: 0.761 Hom.: 2595

Bravo AF: 0.757

Asia WGS AF: 0.911 AC: 3171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.20
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9521337; hg19: chr13-110025636;