chr13-59532791-T-C

Position:

• chr13-59532791-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 0.736 in 152,146 control chromosomes in the GnomAD database, including 47,838 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 0.74 (47838 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.827

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.59532791T>C		intergenic_region
LOC107984625	XR_001749886.2	n.234-1403A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.737 AC: 112007 AN: 152030 Hom.: 47835 Cov.: 33

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.846

Gnomad ASJ AF: 0.858

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.736 AC: 112014 AN: 152146 Hom.: 47838 Cov.: 33 AF XY: 0.739 AC XY: 54995 AN XY: 74398

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.846

Gnomad4 ASJ AF: 0.858

Gnomad4 EAS AF: 0.793

Gnomad4 SAS AF: 0.838

Gnomad4 FIN AF: 0.926

Gnomad4 NFE AF: 0.947

Gnomad4 OTH AF: 0.774

Alfa AF: 0.911 Hom.: 67148

Bravo AF: 0.709

Asia WGS AF: 0.794 AC: 2757 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.36
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1622710; hg19: chr13-60106925;