rs9567349

Variant names:

• chr13-44063269-A-G
• rs9567349

Your query was ambiguous. Multiple possible variants found:

• chr13-44063269-A-G
• chr13-44063269-A-T

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 0.143 in 152,204 control chromosomes in the GnomAD database, including 2,139 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 0.14 (2139 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 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: 0.143 AC: 21765 AN: 152086 Hom.: 2126 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0559

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0917

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0756

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.143 AC: 21811 AN: 152204 Hom.: 2139 Cov.: 32 AF XY: 0.144 AC XY: 10690 AN XY: 74390

African (AFR) AF: 0.276 AC: 11463 AN: 41504

American (AMR) AF: 0.120 AC: 1841 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0559 AC: 194 AN: 3472

East Asian (EAS) AF: 0.213 AC: 1095 AN: 5152

South Asian (SAS) AF: 0.129 AC: 621 AN: 4818

European-Finnish (FIN) AF: 0.0917 AC: 973 AN: 10608

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0756 AC: 5142 AN: 68030

Other (OTH) AF: 0.121 AC: 256 AN: 2116

Alfa AF: 0.106 Hom.: 2000

Bravo AF: 0.151

Asia WGS AF: 0.189 AC: 654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.54
PhyloP100		0.039

Splicing

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

Other links and lift over

dbSNP: rs9567349; hg19: chr13-44637405;