13-23016563-T-G

Variant names:

• chr13-23016563-T-G
• rs9580513

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 0.86 in 152,144 control chromosomes in the GnomAD database, including 56,523 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 0.86 (56523 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 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: 0.860 AC: 130815 AN: 152026 Hom.: 56488 Cov.: 31

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.855

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.880

Gnomad MID AF: 0.904

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.864

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

GnomAD4 genome AF: 0.860 AC: 130910 AN: 152144 Hom.: 56523 Cov.: 31 AF XY: 0.860 AC XY: 63930 AN XY: 74378

African (AFR) AF: 0.806 AC: 33429 AN: 41498

American (AMR) AF: 0.855 AC: 13065 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.830 AC: 2878 AN: 3468

East Asian (EAS) AF: 0.908 AC: 4681 AN: 5156

South Asian (SAS) AF: 0.829 AC: 4006 AN: 4830

European-Finnish (FIN) AF: 0.880 AC: 9302 AN: 10574

Middle Eastern (MID) AF: 0.901 AC: 263 AN: 292

European-Non Finnish (NFE) AF: 0.892 AC: 60674 AN: 68018

Other (OTH) AF: 0.864 AC: 1822 AN: 2110

Alfa AF: 0.875 Hom.: 8339

Bravo AF: 0.857

Asia WGS AF: 0.856 AC: 2979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.3
DANN	Benign	0.63
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9580513; hg19: chr13-23590702;