13-82123686-T-C

Position:

• chr13-82123686-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 0.926 in 152,174 control chromosomes in the GnomAD database, including 65,416 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 0.93 (65416 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.82123686T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.926 AC: 140823 AN: 152056 Hom.: 65347 Cov.: 32

Gnomad AFR AF: 0.981

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.876

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.896

Gnomad OTH AF: 0.911

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

GnomAD4 genome AF: 0.926 AC: 140952 AN: 152174 Hom.: 65416 Cov.: 32 AF XY: 0.927 AC XY: 68942 AN XY: 74400

Gnomad4 AFR AF: 0.981

Gnomad4 AMR AF: 0.936

Gnomad4 ASJ AF: 0.876

Gnomad4 EAS AF: 0.954

Gnomad4 SAS AF: 0.893

Gnomad4 FIN AF: 0.921

Gnomad4 NFE AF: 0.896

Gnomad4 OTH AF: 0.912

Alfa AF: 0.907 Hom.: 7859

Bravo AF: 0.931

Asia WGS AF: 0.938 AC: 3246 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.24
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1331584; hg19: chr13-82697821;