13-22596397-T-C

Variant names:

• chr13-22596397-T-C
• rs9578482

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 0.227 in 152,078 control chromosomes in the GnomAD database, including 4,091 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 0.23 (4091 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 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: 0.227 AC: 34529 AN: 151960 Hom.: 4092 Cov.: 33

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.0932

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.227 AC: 34546 AN: 152078 Hom.: 4091 Cov.: 33 AF XY: 0.227 AC XY: 16849 AN XY: 74362

African (AFR) AF: 0.305 AC: 12629 AN: 41474

American (AMR) AF: 0.200 AC: 3058 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 446 AN: 3470

East Asian (EAS) AF: 0.0930 AC: 482 AN: 5182

South Asian (SAS) AF: 0.176 AC: 845 AN: 4814

European-Finnish (FIN) AF: 0.217 AC: 2296 AN: 10578

Middle Eastern (MID) AF: 0.195 AC: 57 AN: 292

European-Non Finnish (NFE) AF: 0.209 AC: 14193 AN: 67972

Other (OTH) AF: 0.204 AC: 431 AN: 2110

Alfa AF: 0.235 Hom.: 588

Bravo AF: 0.227

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	13
DANN	Benign	0.71
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs9578482; hg19: chr13-23170536;