rs11613092

Positions:

• chr12-118455443-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 0.0806 in 152,096 control chromosomes in the GnomAD database, including 681 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 0.081 (681 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.118455443C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0805 AC: 12231 AN: 151978 Hom.: 672 Cov.: 31

Gnomad AFR AF: 0.0504

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.0476

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.0835

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0690

Gnomad OTH AF: 0.0785

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

GnomAD4 genome AF: 0.0806 AC: 12252 AN: 152096 Hom.: 681 Cov.: 31 AF XY: 0.0848 AC XY: 6303 AN XY: 74330

Gnomad4 AFR AF: 0.0502

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.0476

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.0838

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.0690

Gnomad4 OTH AF: 0.0777

Alfa AF: 0.0725 Hom.: 1103

Bravo AF: 0.0835

Asia WGS AF: 0.126 AC: 437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	13
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11613092; hg19: chr12-118893248;