rs17500692

Variant names:

• chr18-900788-G-A
• rs17500692
• ENST00000582554.1:n.91-6093C>T

Your query was ambiguous. Multiple possible variants found:

• chr18-900788-G-A
• chr18-900788-G-C

Variant summary

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

The ENST00000582554.1(ENSG00000265671):​n.91-6093C>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: ENSG00000265671 ENST00000582554.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

ENSG00000265671 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000265671	ENST00000582554.1	n.91-6093C>T		intron_variant	Intron 1 of 1	5

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

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.0850

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.154

Alfa AF: 0.130 Hom.: 2996

Bravo AF: 0.143

Asia WGS AF: 0.236 AC: 822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17500692; hg19: chr18-900789;