rs11872992

Variant names:

• chr18-60373354-G-A
• rs11872992
• ENST00000650201.1:n.113+44009G>A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The ENST00000650201.1(ENSG00000285681):​n.113+44009G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,116 control chromosomes in the GnomAD database, including 1,500 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).

• Frequency: Genomes: 𝑓 0.12 (1500 hom., cov: 32)
• Consequence: ENSG00000285681 ENST00000650201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

Genes affected

ENSG00000285681 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 18-60373354-G-A is Benign according to our data. Variant chr18-60373354-G-A is described in Lovd as [Likely_benign].
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 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+44009G>A		intron_variant	Intron 1 of 3
ENSG00000285681	ENST00000658928.1	n.156+44009G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18680 AN: 151998 Hom.: 1500 Cov.: 32

Gnomad AFR AF: 0.0329

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.123 AC: 18685 AN: 152116 Hom.: 1500 Cov.: 32 AF XY: 0.129 AC XY: 9603 AN XY: 74336

Gnomad4 AFR AF: 0.0328

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.121

Alfa AF: 0.141 Hom.: 2171

Bravo AF: 0.110

Asia WGS AF: 0.172 AC: 594 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.12
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11872992; hg19: chr18-58040587;