18-60367971-T-G

Variant names:

• chr18-60367971-T-G
• rs1943226
• ENST00000650201.1:n.113+38626T>G

Variant summary

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

The ENST00000650201.1(ENSG00000285681):​n.113+38626T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0675 in 152,130 control chromosomes in the GnomAD database, including 489 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 0.067 (489 hom., cov: 33)
• Consequence: ENSG00000285681 ENST00000650201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

Genes affected

ENSG00000285681 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.117 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+38626T>G		intron_variant	Intron 1 of 3
ENSG00000285681	ENST00000658928.1	n.156+38626T>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0675 AC: 10264 AN: 152012 Hom.: 489 Cov.: 33

Gnomad AFR AF: 0.0152

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0461

Gnomad ASJ AF: 0.0959

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0951

Gnomad OTH AF: 0.0622

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

GnomAD4 genome AF: 0.0675 AC: 10262 AN: 152130 Hom.: 489 Cov.: 33 AF XY: 0.0665 AC XY: 4950 AN XY: 74396

Gnomad4 AFR AF: 0.0152

Gnomad4 AMR AF: 0.0460

Gnomad4 ASJ AF: 0.0959

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.0950

Gnomad4 OTH AF: 0.0616

Alfa AF: 0.0832 Hom.: 814

Bravo AF: 0.0586

Asia WGS AF: 0.0420 AC: 144 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.38
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1943226; hg19: chr18-58035204;