rs11876485

Variant names:

• chr18-22636284-T-C
• rs11876485
• ENST00000716263.1:n.729-23431A>G

Variant summary

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

The ENST00000716263.1(ENSG00000266850):​n.729-23431A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.83 in 152,134 control chromosomes in the GnomAD database, including 52,717 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 0.83 (52717 hom., cov: 32)
• Consequence: ENSG00000266850 ENST00000716263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.828
• Publications: 5 publications found

Genes affected

ENSG00000266850 (HGNC:58091):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.848 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
ENSG00000266850	ENST00000716263.1	n.729-23431A>G		intron_variant	Intron 5 of 6
ENSG00000266850	ENST00000716264.1	n.924-23431A>G		intron_variant	Intron 7 of 8
ENSG00000266850	ENST00000795021.1	n.678-26091A>G		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.830 AC: 126247 AN: 152016 Hom.: 52677 Cov.: 32

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.857

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.898

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.840

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

GnomAD4 genome AF: 0.830 AC: 126340 AN: 152134 Hom.: 52717 Cov.: 32 AF XY: 0.829 AC XY: 61656 AN XY: 74366

African (AFR) AF: 0.813 AC: 33713 AN: 41488

American (AMR) AF: 0.816 AC: 12477 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.857 AC: 2977 AN: 3472

East Asian (EAS) AF: 0.653 AC: 3368 AN: 5158

South Asian (SAS) AF: 0.721 AC: 3478 AN: 4826

European-Finnish (FIN) AF: 0.898 AC: 9514 AN: 10596

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.854 AC: 58025 AN: 67982

Other (OTH) AF: 0.835 AC: 1767 AN: 2116

Alfa AF: 0.841 Hom.: 9363

Bravo AF: 0.826

Asia WGS AF: 0.661 AC: 2299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.83
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs11876485; hg19: chr18-20216247;