rs17500692

Variant names:

• chr18-900788-G-A
• rs17500692
• ENST00000582554.2:n.179-6093C>T

Your query was ambiguous. Multiple possible variants found:

• chr18-900788-G-A
• chr18-900788-G-C

Variant summary

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

The ENST00000582554.2(ENSG00000265179):​n.179-6093C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,136 control chromosomes in the GnomAD database, including 1,766 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 0.15 (1766 hom., cov: 33)
• Consequence: ENSG00000265179 ENST00000582554.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 2 publications found

Genes affected

ENSG00000265179 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000582554.2. 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
	ENSG00000265179	ENST00000582554.2	TSL:5	n.179-6093C>T		intron	N/A
	ENSG00000265179	ENST00000717225.1		n.261+4675C>T		intron	N/A
	ENSG00000265179	ENST00000717226.1		n.340+3361C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22175 AN: 152018 Hom.: 1758 Cov.: 33

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.0851

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.146 AC: 22227 AN: 152136 Hom.: 1766 Cov.: 33 AF XY: 0.145 AC XY: 10781 AN XY: 74360

African (AFR) AF: 0.181 AC: 7522 AN: 41478

American (AMR) AF: 0.0850 AC: 1299 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 495 AN: 3470

East Asian (EAS) AF: 0.236 AC: 1224 AN: 5180

South Asian (SAS) AF: 0.199 AC: 960 AN: 4816

European-Finnish (FIN) AF: 0.112 AC: 1186 AN: 10578

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.131 AC: 8939 AN: 68018

Other (OTH) AF: 0.154 AC: 325 AN: 2110

Alfa AF: 0.134 Hom.: 6398

Bravo AF: 0.143

Asia WGS AF: 0.236 AC: 822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.048
DANN	Benign	0.63
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs17500692; hg19: chr18-900789;