chr13-102876308-A-G

Position:

• chr13-102876308-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 0.0819 in 152,282 control chromosomes in the GnomAD database, including 647 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 0.082 (647 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.102876308A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0820 AC: 12478 AN: 152164 Hom.: 647 Cov.: 33

Gnomad AFR AF: 0.0433

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.0541

Gnomad ASJ AF: 0.0574

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0488

Gnomad FIN AF: 0.0876

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.0645

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

GnomAD4 genome AF: 0.0819 AC: 12476 AN: 152282 Hom.: 647 Cov.: 33 AF XY: 0.0775 AC XY: 5772 AN XY: 74450

Gnomad4 AFR AF: 0.0432

Gnomad4 AMR AF: 0.0540

Gnomad4 ASJ AF: 0.0574

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0487

Gnomad4 FIN AF: 0.0876

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.0629

Alfa AF: 0.102 Hom.: 866

Bravo AF: 0.0771

Asia WGS AF: 0.0200 AC: 69 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.1
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4150393; hg19: chr13-103528658;