11-113493925-G-T

Position:

• chr11-113493925-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 0.719 in 151,994 control chromosomes in the GnomAD database, including 40,019 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 0.72 (40019 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.113493925G>T		intergenic_region
LOC105369501	XR_948024.2	n.107-2735C>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109114 AN: 151876 Hom.: 39957 Cov.: 31

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.719 AC: 109239 AN: 151994 Hom.: 40019 Cov.: 31 AF XY: 0.729 AC XY: 54168 AN XY: 74296

Gnomad4 AFR AF: 0.824

Gnomad4 AMR AF: 0.682

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.974

Gnomad4 SAS AF: 0.757

Gnomad4 FIN AF: 0.822

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.657

Alfa AF: 0.620 Hom.: 4380

Bravo AF: 0.709

Asia WGS AF: 0.867 AC: 3012 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4245150; hg19: chr11-113364647;