18-24876381-C-T

Variant names:

• chr18-24876381-C-T
• rs10502460
• ENST00000577354.6:n.562-33407C>T

Variant summary

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

The ENST00000577354.6(ENSG00000266573):​n.562-33407C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0834 in 152,146 control chromosomes in the GnomAD database, including 1,334 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 0.083 (1334 hom., cov: 33)
• Consequence: ENSG00000266573 ENST00000577354.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.78

Genes affected

ENSG00000266573 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.369 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
ENSG00000266573	ENST00000577354.6	n.562-33407C>T		intron_variant	Intron 3 of 3	4
ENSG00000266573	ENST00000582650.5	n.236-51457C>T		intron_variant	Intron 2 of 3	4
ENSG00000266573	ENST00000654065.1	n.227-59601C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0833 AC: 12663 AN: 152028 Hom.: 1332 Cov.: 33

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0161

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00387

Gnomad OTH AF: 0.0584

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

GnomAD4 genome AF: 0.0834 AC: 12684 AN: 152146 Hom.: 1334 Cov.: 33 AF XY: 0.0874 AC XY: 6498 AN XY: 74366

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.00202

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.0161

Gnomad4 NFE AF: 0.00387

Gnomad4 OTH AF: 0.0592

Alfa AF: 0.0507 Hom.: 109

Bravo AF: 0.0952

Asia WGS AF: 0.196 AC: 682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.018
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10502460; hg19: chr18-22456345;