18-1575019-A-G

Variant names:

• chr18-1575019-A-G
• rs17384005
• ENST00000583163.2:n.335+8495A>G

Variant summary

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

The ENST00000583163.2(ENSG00000266602):​n.335+8495A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,126 control chromosomes in the GnomAD database, including 1,404 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 0.13 (1404 hom., cov: 32)
• Consequence: ENSG00000266602 ENST00000583163.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.199
• Publications: 2 publications found

Genes affected

ENSG00000266602 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000583163.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000266602	ENST00000583163.2	TSL:2	n.335+8495A>G		intron	N/A
	ENSG00000266602	ENST00000652957.2		n.275+8495A>G		intron	N/A
	ENSG00000266602	ENST00000653006.1		n.311+8495A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19287 AN: 152008 Hom.: 1401 Cov.: 32

Gnomad AFR AF: 0.0727

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.0896

Gnomad EAS AF: 0.00828

Gnomad SAS AF: 0.0740

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.127 AC: 19301 AN: 152126 Hom.: 1404 Cov.: 32 AF XY: 0.123 AC XY: 9135 AN XY: 74364

African (AFR) AF: 0.0727 AC: 3021 AN: 41526

American (AMR) AF: 0.151 AC: 2303 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0896 AC: 311 AN: 3470

East Asian (EAS) AF: 0.00849 AC: 44 AN: 5180

South Asian (SAS) AF: 0.0743 AC: 358 AN: 4820

European-Finnish (FIN) AF: 0.145 AC: 1542 AN: 10600

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.165 AC: 11205 AN: 67960

Other (OTH) AF: 0.122 AC: 257 AN: 2098

Alfa AF: 0.148 Hom.: 2541

Bravo AF: 0.125

Asia WGS AF: 0.0390 AC: 137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.63
DANN	Benign	0.44
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs17384005; hg19: chr18-1575020;