18-11373581-G-A

Variant names:

• chr18-11373581-G-A
• rs10502411
• ENST00000592198.1:n.155+4674C>T

Variant summary

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

The ENST00000592198.1(ENSG00000267051):​n.155+4674C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0818 in 152,230 control chromosomes in the GnomAD database, including 1,161 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 0.082 (1161 hom., cov: 32)
• Consequence: ENSG00000267051 ENST00000592198.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104
• Publications: 0 publications found

Genes affected

ENSG00000267051 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000592198.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267051	ENST00000592198.1	TSL:3	n.155+4674C>T		intron	N/A
	ENSG00000267051	ENST00000765726.1		n.319-36513C>T		intron	N/A
	ENSG00000267051	ENST00000765727.1		n.319-36513C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0818 AC: 12450 AN: 152112 Hom.: 1164 Cov.: 32

Gnomad AFR AF: 0.0371

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.0662

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0494

Gnomad OTH AF: 0.0832

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

GnomAD4 genome AF: 0.0818 AC: 12455 AN: 152230 Hom.: 1161 Cov.: 32 AF XY: 0.0896 AC XY: 6668 AN XY: 74446

African (AFR) AF: 0.0371 AC: 1539 AN: 41534

American (AMR) AF: 0.186 AC: 2845 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0662 AC: 230 AN: 3472

East Asian (EAS) AF: 0.471 AC: 2443 AN: 5184

South Asian (SAS) AF: 0.142 AC: 685 AN: 4828

European-Finnish (FIN) AF: 0.102 AC: 1077 AN: 10588

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0494 AC: 3360 AN: 68006

Other (OTH) AF: 0.0847 AC: 179 AN: 2114

Alfa AF: 0.0653 Hom.: 80

Bravo AF: 0.0875

Asia WGS AF: 0.254 AC: 883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.23
DANN	Benign	0.75
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs10502411; hg19: chr18-11373580;