chr13-105065312-A-G

Position:

• chr13-105065312-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.666 in 151,848 control chromosomes in the GnomAD database, including 34,280 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 (34280 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.715

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.105065312A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101031 AN: 151730 Hom.: 34252 Cov.: 30

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.666 AC: 101100 AN: 151848 Hom.: 34280 Cov.: 30 AF XY: 0.670 AC XY: 49696 AN XY: 74176

Gnomad4 AFR AF: 0.760

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.933

Gnomad4 SAS AF: 0.768

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.610

Gnomad4 OTH AF: 0.655

Alfa AF: 0.629 Hom.: 14246

Bravo AF: 0.658

Asia WGS AF: 0.827 AC: 2876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7139453; hg19: chr13-105717663;