18-32841011-A-G

Variant names:

• chr18-32841011-A-G
• rs1941286
• ENST00000580366.1:n.27+5820A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000580366.1(ENSG00000263765):​n.27+5820A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.882 in 152,178 control chromosomes in the GnomAD database, including 61,144 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 0.88 (61144 hom., cov: 31)
• Consequence: ENSG00000263765 ENST00000580366.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.404
• Publications: 1 publications found

Genes affected

ENSG00000263765 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000580366.1. 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
	ENSG00000263765	ENST00000580366.1	TSL:3	n.27+5820A>G		intron	N/A
	ENSG00000263765	ENST00000582239.1	TSL:5	n.393+5820A>G		intron	N/A
	ENSG00000263765	ENST00000798721.1		n.98+7488A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.882 AC: 134153 AN: 152060 Hom.: 61125 Cov.: 31

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.981

Gnomad AMR AF: 0.943

Gnomad ASJ AF: 0.986

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.982

Gnomad FIN AF: 0.968

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.913

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

GnomAD4 genome AF: 0.882 AC: 134225 AN: 152178 Hom.: 61144 Cov.: 31 AF XY: 0.884 AC XY: 65795 AN XY: 74400

African (AFR) AF: 0.627 AC: 26013 AN: 41460

American (AMR) AF: 0.943 AC: 14427 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.986 AC: 3421 AN: 3468

East Asian (EAS) AF: 0.991 AC: 5114 AN: 5162

South Asian (SAS) AF: 0.983 AC: 4740 AN: 4824

European-Finnish (FIN) AF: 0.968 AC: 10279 AN: 10620

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.987 AC: 67134 AN: 68032

Other (OTH) AF: 0.912 AC: 1927 AN: 2112

Alfa AF: 0.916 Hom.: 8110

Asia WGS AF: 0.953 AC: 3314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	11
DANN	Benign	0.73
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs1941286; hg19: chr18-30420974;