rs9531843

Variant names:

• chr13-85808985-G-A
• rs9531843

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 0.365 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.165 AC: 6839 AN: 41470

American (AMR) AF: 0.402 AC: 6135 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1242 AN: 3466

East Asian (EAS) AF: 0.610 AC: 3131 AN: 5134

South Asian (SAS) AF: 0.429 AC: 2065 AN: 4814

European-Finnish (FIN) AF: 0.432 AC: 4555 AN: 10544

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30109 AN: 67930

Other (OTH) AF: 0.385 AC: 811 AN: 2104

Alfa AF: 0.417 Hom.: 20127

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
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs9531843; hg19: chr13-86383120;