rs11873305

Variant names:

• chr18-60381959-A-C
• rs11873305
• ENST00000650201.1:n.113+52614A>C

Variant summary

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

The ENST00000650201.1(ENSG00000285681):​n.113+52614A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,162 control chromosomes in the GnomAD database, including 1,979 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 (1979 hom., cov: 31)
• Consequence: ENSG00000285681 ENST00000650201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.462
• Publications: 26 publications found

Genes affected

ENSG00000285681 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.299 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
ENSG00000285681	ENST00000650201.1	n.113+52614A>C		intron_variant	Intron 1 of 3
ENSG00000285681	ENST00000658928.1	n.156+52614A>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16693 AN: 152044 Hom.: 1963 Cov.: 31

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0491

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0357

Gnomad FIN AF: 0.0282

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0384

Gnomad OTH AF: 0.0850

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

GnomAD4 genome AF: 0.110 AC: 16744 AN: 152162 Hom.: 1979 Cov.: 31 AF XY: 0.106 AC XY: 7922 AN XY: 74412

African (AFR) AF: 0.304 AC: 12587 AN: 41456

American (AMR) AF: 0.0490 AC: 749 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3468

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5186

South Asian (SAS) AF: 0.0347 AC: 167 AN: 4814

European-Finnish (FIN) AF: 0.0282 AC: 299 AN: 10610

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0384 AC: 2613 AN: 68010

Other (OTH) AF: 0.0841 AC: 178 AN: 2116

Alfa AF: 0.0741 Hom.: 1832

Bravo AF: 0.121

Asia WGS AF: 0.0320 AC: 110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.85
DANN	Benign	0.48
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs11873305; hg19: chr18-58049192;