11-118870448-T-C

Variant names:

• chr11-118870448-T-C
• rs7117261
• ENST00000816613.1:n.16A>G

Variant summary

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

The ENST00000816613.1(ENSG00000306274):​n.16A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.8 in 152,110 control chromosomes in the GnomAD database, including 48,669 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 0.80 (48669 hom., cov: 31)
• Consequence: ENSG00000306274 ENST00000816613.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400
• Publications: 15 publications found

Genes affected

ENSG00000306274 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.857 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
ENSG00000306274	ENST00000816613.1	n.16A>G		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000306274	ENST00000816614.1	n.164A>G		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000306274	ENST00000816615.1	n.172A>G		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.800 AC: 121565 AN: 151992 Hom.: 48642 Cov.: 31

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.802

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.800 AC: 121645 AN: 152110 Hom.: 48669 Cov.: 31 AF XY: 0.803 AC XY: 59670 AN XY: 74344

African (AFR) AF: 0.760 AC: 31537 AN: 41486

American (AMR) AF: 0.824 AC: 12588 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.826 AC: 2865 AN: 3470

East Asian (EAS) AF: 0.878 AC: 4535 AN: 5164

South Asian (SAS) AF: 0.845 AC: 4073 AN: 4818

European-Finnish (FIN) AF: 0.838 AC: 8871 AN: 10584

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

European-Non Finnish (NFE) AF: 0.802 AC: 54512 AN: 67990

Other (OTH) AF: 0.822 AC: 1740 AN: 2116

Alfa AF: 0.799 Hom.: 6039

Bravo AF: 0.800

Asia WGS AF: 0.855 AC: 2974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.1
DANN	Benign	0.34
PhyloP100		0.0040

Splicing

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

Other links and lift over

dbSNP: rs7117261; hg19: chr11-118741157;