chr11-118827828-G-A

Variant names:

• chr11-118827828-G-A
• rs638893
• ENST00000816613.1:n.125-10318C>T

Variant summary

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

The ENST00000816613.1(ENSG00000306274):​n.125-10318C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.789 in 152,146 control chromosomes in the GnomAD database, including 47,921 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 (47921 hom., cov: 32)
• Consequence: ENSG00000306274 ENST00000816613.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243
• Publications: 30 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816613.1. 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
	ENSG00000306274	ENST00000816613.1		n.125-10318C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.789 AC: 119972 AN: 152028 Hom.: 47881 Cov.: 32

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.789 AC: 120065 AN: 152146 Hom.: 47921 Cov.: 32 AF XY: 0.791 AC XY: 58833 AN XY: 74368

African (AFR) AF: 0.660 AC: 27356 AN: 41476

American (AMR) AF: 0.860 AC: 13120 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.846 AC: 2934 AN: 3470

East Asian (EAS) AF: 0.861 AC: 4454 AN: 5176

South Asian (SAS) AF: 0.801 AC: 3866 AN: 4826

European-Finnish (FIN) AF: 0.848 AC: 8984 AN: 10594

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.832 AC: 56569 AN: 68030

Other (OTH) AF: 0.820 AC: 1734 AN: 2114

Alfa AF: 0.815 Hom.: 92771

Bravo AF: 0.784

Asia WGS AF: 0.827 AC: 2876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.33
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs638893; hg19: chr11-118698537;