rs9521354

Variant names:

• chr13-109414777-C-A
• rs9521354

Your query was ambiguous. Multiple possible variants found:

• chr13-109414777-C-A
• chr13-109414777-C-G

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 0.805 in 151,766 control chromosomes in the GnomAD database, including 50,001 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 0.80 (50001 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• 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: 0.805 AC: 122015 AN: 151648 Hom.: 49964 Cov.: 29

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.805 AC: 122102 AN: 151766 Hom.: 50001 Cov.: 29 AF XY: 0.806 AC XY: 59770 AN XY: 74128

Gnomad4 AFR AF: 0.635

Gnomad4 AMR AF: 0.868

Gnomad4 ASJ AF: 0.780

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.825

Gnomad4 FIN AF: 0.875

Gnomad4 NFE AF: 0.866

Gnomad4 OTH AF: 0.800

Alfa AF: 0.848 Hom.: 27448

Bravo AF: 0.799

Asia WGS AF: 0.917 AC: 3191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.34
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9521354; hg19: chr13-110067124;