rs532241

Variant names:

• chr18-10140632-T-G
• rs532241
• ENST00000582470.1:n.163-3525T>G

Variant summary

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

The ENST00000582470.1(ENSG00000265554):​n.163-3525T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 151,734 control chromosomes in the GnomAD database, including 19,360 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 0.50 (19360 hom., cov: 31)
• Consequence: ENSG00000265554 ENST00000582470.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

Genes affected

ENSG00000265554 (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 (SAS) allele frequency at 95% confidence interval = 0.636 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
ENSG00000265554	ENST00000582470.1	n.163-3525T>G		intron_variant	Intron 1 of 1	3
ENSG00000265554	ENST00000669473.1	n.423-3525T>G		intron_variant	Intron 2 of 2
ENSG00000265554	ENST00000685786.1	n.389-3525T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75604 AN: 151616 Hom.: 19323 Cov.: 31

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.499 AC: 75684 AN: 151734 Hom.: 19360 Cov.: 31 AF XY: 0.502 AC XY: 37230 AN XY: 74122

Gnomad4 AFR AF: 0.601

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.640

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.504

Alfa AF: 0.448 Hom.: 14869

Bravo AF: 0.502

Asia WGS AF: 0.657 AC: 2284 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	0.82
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs532241; hg19: chr18-10140629;