18-24534000-T-C

Variant names:

• chr18-24534000-T-C
• rs1972602
• ENST00000581648.2:n.1310+6714A>G

Variant summary

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

The ENST00000581648.2(ENSG00000266489):​n.1310+6714A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 148,910 control chromosomes in the GnomAD database, including 50,866 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 0.82 (50866 hom., cov: 24)
• Consequence: ENSG00000266489 ENST00000581648.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.719

Genes affected

ENSG00000266489 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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
ENSG00000266489	ENST00000581648.2	n.1310+6714A>G		intron_variant	Intron 1 of 2	3
ENSG00000266489	ENST00000662616.1	n.366+9789A>G		intron_variant	Intron 1 of 1
ENSG00000266489	ENST00000668994.1	n.356+9789A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.821 AC: 122179 AN: 148800 Hom.: 50808 Cov.: 24

Gnomad AFR AF: 0.942

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.786

Gnomad MID AF: 0.806

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.821 AC: 122294 AN: 148910 Hom.: 50866 Cov.: 24 AF XY: 0.826 AC XY: 59748 AN XY: 72376

Gnomad4 AFR AF: 0.942

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.846

Gnomad4 FIN AF: 0.786

Gnomad4 NFE AF: 0.739

Gnomad4 OTH AF: 0.802

Alfa AF: 0.685 Hom.: 1908

Bravo AF: 0.833

Asia WGS AF: 0.925 AC: 3217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1972602; hg19: chr18-22113964;