13-76942617-A-G

Position:

• chr13-76942617-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 0.747 in 152,074 control chromosomes in the GnomAD database, including 43,189 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 0.75 (43189 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.76942617A>G		intergenic_region
LOC105370269	XR_001749929.1	n.323+144T>C		intron_variant
LOC105370269	XR_942104.2	n.200+144T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113559 AN: 151954 Hom.: 43172 Cov.: 31

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.813

Gnomad OTH AF: 0.771

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

GnomAD4 genome AF: 0.747 AC: 113622 AN: 152074 Hom.: 43189 Cov.: 31 AF XY: 0.743 AC XY: 55229 AN XY: 74352

Gnomad4 AFR AF: 0.630

Gnomad4 AMR AF: 0.825

Gnomad4 ASJ AF: 0.855

Gnomad4 EAS AF: 0.640

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.778

Gnomad4 NFE AF: 0.813

Gnomad4 OTH AF: 0.770

Alfa AF: 0.801 Hom.: 84637

Bravo AF: 0.751

Asia WGS AF: 0.592 AC: 2058 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	1.6
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs614171; hg19: chr13-77516752;