chr13-113575077-G-A

Variant names:

• chr13-113575077-G-A
• rs80186078

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 0.016 in 152,148 control chromosomes in the GnomAD database, including 68 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 0.016 (68 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.829
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.107 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: 0.0158 AC: 2403 AN: 152030 Hom.: 63 Cov.: 32

Gnomad AFR AF: 0.0334

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.00714

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.0145

Gnomad FIN AF: 0.00425

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00231

Gnomad OTH AF: 0.0154

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

GnomAD4 genome AF: 0.0160 AC: 2440 AN: 152148 Hom.: 68 Cov.: 32 AF XY: 0.0166 AC XY: 1232 AN XY: 74394

African (AFR) AF: 0.0341 AC: 1415 AN: 41512

American (AMR) AF: 0.00719 AC: 110 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00173 AC: 6 AN: 3470

East Asian (EAS) AF: 0.114 AC: 593 AN: 5184

South Asian (SAS) AF: 0.0141 AC: 68 AN: 4812

European-Finnish (FIN) AF: 0.00425 AC: 45 AN: 10590

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00231 AC: 157 AN: 67976

Other (OTH) AF: 0.0171 AC: 36 AN: 2104

Alfa AF: 0.0122 Hom.: 7

Bravo AF: 0.0174

Asia WGS AF: 0.0560 AC: 192 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	11
DANN	Benign	0.87
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs80186078; hg19: chr13-114229392;