rs9531843

Variant names:

• chr13-85808985-G-A
• rs9531843

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 0.365 in 151,914 control chromosomes in the GnomAD database, including 11,493 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 0.37 (11493 hom., cov: 31)
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 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: 0.365 AC: 55466 AN: 151796 Hom.: 11482 Cov.: 31

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.365 AC: 55499 AN: 151914 Hom.: 11493 Cov.: 31 AF XY: 0.367 AC XY: 27242 AN XY: 74216

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.385

Alfa AF: 0.387 Hom.: 3166

Bravo AF: 0.354

Asia WGS AF: 0.495 AC: 1719 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9531843; hg19: chr13-86383120;