13-80065389-T-C

Position:

• chr13-80065389-T-C

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 0.658 in 152,072 control chromosomes in the GnomAD database, including 33,514 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 0.66 (33514 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.80065389T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000284196	ENST00000639897.1	n.224+4390A>G		intron_variant		5
ENSG00000284196	ENST00000639964.1	n.357+4390A>G		intron_variant		4
ENSG00000284196	ENST00000639965.1	n.214+8000A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99934 AN: 151956 Hom.: 33485 Cov.: 32

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.893

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.658 AC: 100007 AN: 152072 Hom.: 33514 Cov.: 32 AF XY: 0.660 AC XY: 49060 AN XY: 74338

Gnomad4 AFR AF: 0.537

Gnomad4 AMR AF: 0.761

Gnomad4 ASJ AF: 0.784

Gnomad4 EAS AF: 0.893

Gnomad4 SAS AF: 0.830

Gnomad4 FIN AF: 0.597

Gnomad4 NFE AF: 0.680

Gnomad4 OTH AF: 0.692

Alfa AF: 0.683 Hom.: 18745

Bravo AF: 0.664

Asia WGS AF: 0.832 AC: 2893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.8
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7990916; hg19: chr13-80639524;