ENST00000650201.1:n.113+39925G>A

Variant names:

• chr18-60369270-G-A
• rs8093815
• ENST00000650201.1:n.113+39925G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650201.1(ENSG00000285681):​n.113+39925G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,012 control chromosomes in the GnomAD database, including 8,780 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 0.33 (8780 hom., cov: 32)
• Consequence: ENSG00000285681 ENST00000650201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84

Genes affected

ENSG00000285681 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.445 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+39925G>A		intron_variant	Intron 1 of 3
ENSG00000285681	ENST00000658928.1	n.156+39925G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49673 AN: 151894 Hom.: 8754 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.327 AC: 49734 AN: 152012 Hom.: 8780 Cov.: 32 AF XY: 0.319 AC XY: 23705 AN XY: 74280

Gnomad4 AFR AF: 0.451

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.315

Alfa AF: 0.309 Hom.: 7287

Bravo AF: 0.344

Asia WGS AF: 0.209 AC: 728 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	0.023
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8093815; hg19: chr18-58036503;