rs11176733

Variant names:

• chr12-67420117-C-T
• rs11176733
• ENST00000791334.1:n.435-1040C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000791334.1(ENSG00000303038):​n.435-1040C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,104 control chromosomes in the GnomAD database, including 1,347 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 0.11 (1347 hom., cov: 31)
• Consequence: ENSG00000303038 ENST00000791334.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.428
• Publications: 2 publications found

Genes affected

ENSG00000303038 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000791334.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303038	ENST00000791334.1		n.435-1040C>T		intron	N/A
	ENSG00000303038	ENST00000791335.1		n.240-1040C>T		intron	N/A
	ENSG00000303038	ENST00000791336.1		n.298-1040C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16791 AN: 151988 Hom.: 1335 Cov.: 31

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.0641

Gnomad ASJ AF: 0.0769

Gnomad EAS AF: 0.0239

Gnomad SAS AF: 0.0499

Gnomad FIN AF: 0.0738

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0689

Gnomad OTH AF: 0.0809

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

GnomAD4 genome AF: 0.111 AC: 16830 AN: 152104 Hom.: 1347 Cov.: 31 AF XY: 0.108 AC XY: 8039 AN XY: 74350

African (AFR) AF: 0.228 AC: 9450 AN: 41466

American (AMR) AF: 0.0639 AC: 978 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0769 AC: 267 AN: 3472

East Asian (EAS) AF: 0.0236 AC: 122 AN: 5176

South Asian (SAS) AF: 0.0497 AC: 239 AN: 4808

European-Finnish (FIN) AF: 0.0738 AC: 780 AN: 10576

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0689 AC: 4684 AN: 67996

Other (OTH) AF: 0.0801 AC: 169 AN: 2110

Alfa AF: 0.0894 Hom.: 1414

Bravo AF: 0.114

Asia WGS AF: 0.0460 AC: 159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.0
DANN	Benign	0.65
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs11176733; hg19: chr12-67813897;