rs9527419

Variant names:

• chr13-55584874-T-A
• rs9527419

Your query was ambiguous. Multiple possible variants found:

• chr13-55584874-T-A
• chr13-55584874-T-C
• chr13-55584874-T-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 0.811 in 152,188 control chromosomes in the GnomAD database, including 50,221 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 0.81 (50221 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.443

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 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: 0.811 AC: 123300 AN: 152070 Hom.: 50186 Cov.: 33

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.811 AC: 123393 AN: 152188 Hom.: 50221 Cov.: 33 AF XY: 0.814 AC XY: 60574 AN XY: 74418

Gnomad4 AFR AF: 0.780

Gnomad4 AMR AF: 0.871

Gnomad4 ASJ AF: 0.822

Gnomad4 EAS AF: 0.944

Gnomad4 SAS AF: 0.705

Gnomad4 FIN AF: 0.865

Gnomad4 NFE AF: 0.803

Gnomad4 OTH AF: 0.825

Alfa AF: 0.803 Hom.: 6095

Bravo AF: 0.818

Asia WGS AF: 0.810 AC: 2807 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9527419; hg19: chr13-56159009; COSMIC: COSV69351980;