11-113482039-G-T

Position:

• chr11-113482039-G-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 0.208 in 152,104 control chromosomes in the GnomAD database, including 3,629 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 0.21 (3629 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.908

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.113482039G>T		intergenic_region
LOC105369501	XR_948024.2	n.379-2466C>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31561 AN: 151986 Hom.: 3613 Cov.: 33

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.208 AC: 31616 AN: 152104 Hom.: 3629 Cov.: 33 AF XY: 0.213 AC XY: 15843 AN XY: 74354

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.196

Alfa AF: 0.170 Hom.: 2187

Bravo AF: 0.213

Asia WGS AF: 0.329 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.8
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10891556; hg19: chr11-113352761;