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. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.635 AC: 26206 AN: 41294

American (AMR) AF: 0.868 AC: 13254 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.780 AC: 2703 AN: 3466

East Asian (EAS) AF: 0.999 AC: 5159 AN: 5164

South Asian (SAS) AF: 0.825 AC: 3969 AN: 4812

European-Finnish (FIN) AF: 0.875 AC: 9157 AN: 10468

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.866 AC: 58893 AN: 67980

Other (OTH) AF: 0.800 AC: 1686 AN: 2108

Alfa AF: 0.847 Hom.: 30453

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
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs9521354; hg19: chr13-110067124;