13-94982059-T-C

Position:

• chr13-94982059-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 0.893 in 152,200 control chromosomes in the GnomAD database, including 62,478 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 0.89 (62478 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.99 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.94982059T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287635	ENST00000669430.1	n.73-20280A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.894 AC: 135923 AN: 152082 Hom.: 62462 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.956

Gnomad ASJ AF: 0.976

Gnomad EAS AF: 0.967

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.917

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

GnomAD4 genome AF: 0.893 AC: 135989 AN: 152200 Hom.: 62478 Cov.: 32 AF XY: 0.895 AC XY: 66611 AN XY: 74426

Gnomad4 AFR AF: 0.653

Gnomad4 AMR AF: 0.956

Gnomad4 ASJ AF: 0.976

Gnomad4 EAS AF: 0.967

Gnomad4 SAS AF: 0.908

Gnomad4 FIN AF: 0.999

Gnomad4 NFE AF: 0.996

Gnomad4 OTH AF: 0.918

Alfa AF: 0.980 Hom.: 131783

Bravo AF: 0.882

Asia WGS AF: 0.922 AC: 3202 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2148065; hg19: chr13-95634313;