rs11613092

Variant names:

• chr12-118455443-C-T
• rs11613092

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0502 AC: 2084 AN: 41484

American (AMR) AF: 0.178 AC: 2721 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0476 AC: 165 AN: 3466

East Asian (EAS) AF: 0.137 AC: 706 AN: 5166

South Asian (SAS) AF: 0.0838 AC: 404 AN: 4820

European-Finnish (FIN) AF: 0.122 AC: 1292 AN: 10572

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0690 AC: 4692 AN: 68006

Other (OTH) AF: 0.0777 AC: 164 AN: 2110

Alfa AF: 0.0737 Hom.: 1857

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
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs11613092; hg19: chr12-118893248;