ENST00000650201.1:n.113+57473T>G

Variant names:

• chr18-60386818-T-G
• rs1943225
• ENST00000650201.1:n.113+57473T>G

Variant summary

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

The ENST00000650201.1(ENSG00000285681):​n.113+57473T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 151,102 control chromosomes in the GnomAD database, including 2,845 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 0.18 (2845 hom., cov: 32)
• Consequence: ENSG00000285681 ENST00000650201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.231 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+57473T>G		intron_variant	Intron 1 of 3
ENSG00000285681	ENST00000658928.1	n.156+57473T>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26728 AN: 150986 Hom.: 2845 Cov.: 32

Gnomad AFR AF: 0.0672

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.0995

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.177 AC: 26724 AN: 151102 Hom.: 2845 Cov.: 32 AF XY: 0.173 AC XY: 12791 AN XY: 73834

African (AFR) AF: 0.0671 AC: 2760 AN: 41120

American (AMR) AF: 0.213 AC: 3216 AN: 15114

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 686 AN: 3456

East Asian (EAS) AF: 0.0997 AC: 511 AN: 5124

South Asian (SAS) AF: 0.207 AC: 993 AN: 4790

European-Finnish (FIN) AF: 0.188 AC: 1983 AN: 10532

Middle Eastern (MID) AF: 0.188 AC: 55 AN: 292

European-Non Finnish (NFE) AF: 0.234 AC: 15850 AN: 67678

Other (OTH) AF: 0.188 AC: 392 AN: 2088

Alfa AF: 0.220 Hom.: 6360

Bravo AF: 0.179

Asia WGS AF: 0.141 AC: 489 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.18
DANN	Benign	0.74
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1943225; hg19: chr18-58054051;