rs13191343

Positions:

• chr6-31273332-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 0.132 in 151,976 control chromosomes in the GnomAD database, including 1,486 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 0.13 (1486 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214

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 (SAS) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.31273332C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20015 AN: 151856 Hom.: 1483 Cov.: 30

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.132 AC: 20026 AN: 151976 Hom.: 1486 Cov.: 30 AF XY: 0.134 AC XY: 9935 AN XY: 74298

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.136

Alfa AF: 0.133 Hom.: 140

Bravo AF: 0.129

Asia WGS AF: 0.141 AC: 490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.7
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13191343; hg19: chr6-31241109;