chr13-22385991-G-A

Variant names:

• chr13-22385991-G-A
• rs9510171

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 0.675 in 152,166 control chromosomes in the GnomAD database, including 40,805 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 0.67 (40805 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.876 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: 0.675 AC: 102645 AN: 152048 Hom.: 40804 Cov.: 33

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.962

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.675 AC: 102651 AN: 152166 Hom.: 40805 Cov.: 33 AF XY: 0.677 AC XY: 50308 AN XY: 74356

African (AFR) AF: 0.222 AC: 9224 AN: 41482

American (AMR) AF: 0.729 AC: 11141 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.874 AC: 3034 AN: 3470

East Asian (EAS) AF: 0.709 AC: 3659 AN: 5160

South Asian (SAS) AF: 0.837 AC: 4045 AN: 4832

European-Finnish (FIN) AF: 0.839 AC: 8905 AN: 10614

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.882 AC: 60002 AN: 68002

Other (OTH) AF: 0.721 AC: 1525 AN: 2114

Alfa AF: 0.800 Hom.: 110924

Bravo AF: 0.641

Asia WGS AF: 0.737 AC: 2564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.4
DANN	Benign	0.88
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9510171; hg19: chr13-22960130;