11-118871133-C-T

Variant names:

• chr11-118871133-C-T
• rs4938573
• ENST00000816968.1:n.*58C>T

Variant summary

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

The ENST00000816968.1(ENSG00000306318):​n.*58C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.792 in 150,166 control chromosomes in the GnomAD database, including 46,966 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 0.79 (46966 hom., cov: 25)
• Consequence: ENSG00000306318 ENST00000816968.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 51 publications found

Genes affected

ENSG00000306318 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816968.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306318	ENST00000816968.1		n.*58C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.792 AC: 118800 AN: 150054 Hom.: 46939 Cov.: 25

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.827

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.843

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.813

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

GnomAD4 genome AF: 0.792 AC: 118879 AN: 150166 Hom.: 46966 Cov.: 25 AF XY: 0.796 AC XY: 58258 AN XY: 73224

African (AFR) AF: 0.725 AC: 29455 AN: 40610

American (AMR) AF: 0.826 AC: 12386 AN: 14998

Ashkenazi Jewish (ASJ) AF: 0.827 AC: 2858 AN: 3456

East Asian (EAS) AF: 0.879 AC: 4487 AN: 5104

South Asian (SAS) AF: 0.853 AC: 4014 AN: 4704

European-Finnish (FIN) AF: 0.843 AC: 8698 AN: 10314

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.803 AC: 54360 AN: 67702

Other (OTH) AF: 0.815 AC: 1696 AN: 2080

Alfa AF: 0.801 Hom.: 212694

Bravo AF: 0.786

Asia WGS AF: 0.852 AC: 2963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.0020
DANN	Benign	0.75
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs4938573; hg19: chr11-118741842;