chr13-71313177-C-T

Position:

• chr13-71313177-C-T

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 0.829 in 151,690 control chromosomes in the GnomAD database, including 52,278 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 0.83 (52278 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.496

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.71313177C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.829 AC: 125716 AN: 151572 Hom.: 52251 Cov.: 32

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.838

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.829 AC: 125795 AN: 151690 Hom.: 52278 Cov.: 32 AF XY: 0.833 AC XY: 61785 AN XY: 74180

Gnomad4 AFR AF: 0.761

Gnomad4 AMR AF: 0.845

Gnomad4 ASJ AF: 0.838

Gnomad4 EAS AF: 0.891

Gnomad4 SAS AF: 0.831

Gnomad4 FIN AF: 0.929

Gnomad4 NFE AF: 0.848

Gnomad4 OTH AF: 0.818

Alfa AF: 0.842 Hom.: 8144

Bravo AF: 0.818

Asia WGS AF: 0.848 AC: 2945 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	13
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2480555; hg19: chr13-71887309;