rs8087522

Variant names:

• chr18-60373245-G-A
• rs8087522
• ENST00000650201.1:n.113+43900G>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+43900G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,896 control chromosomes in the GnomAD database, including 12,477 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 0.38 (12477 hom., cov: 32)
• Consequence: ENSG00000285681 ENST00000650201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655

Genes affected

ENSG00000285681 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 18-60373245-G-A is Benign according to our data. Variant chr18-60373245-G-A is described in Lovd as [Likely_benign].
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.592 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+43900G>A		intron_variant	Intron 1 of 3
ENSG00000285681	ENST00000658928.1	n.156+43900G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57467 AN: 151776 Hom.: 12442 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.379 AC: 57541 AN: 151896 Hom.: 12477 Cov.: 32 AF XY: 0.370 AC XY: 27464 AN XY: 74216

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.345

Alfa AF: 0.354 Hom.: 1875

Bravo AF: 0.397

Asia WGS AF: 0.235 AC: 816 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.36
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8087522; hg19: chr18-58040478;