18-1690050-C-T

Variant names:

• chr18-1690050-C-T
• rs1975743
• ENST00000580524.1:n.408+33555C>T

Variant summary

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

The ENST00000580524.1(ENSG00000266602):​n.408+33555C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.735 in 152,100 control chromosomes in the GnomAD database, including 41,807 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 0.73 (41807 hom., cov: 33)
• Consequence: ENSG00000266602 ENST00000580524.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 1 publications found

Genes affected

ENSG00000266602 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.878 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
ENSG00000266602	ENST00000580524.1	n.408+33555C>T		intron_variant	Intron 2 of 2	3
ENSG00000266602	ENST00000653006.1	n.440+63683C>T		intron_variant	Intron 4 of 4
ENSG00000266602	ENST00000653094.1	n.252-553C>T		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111688 AN: 151982 Hom.: 41759 Cov.: 33

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.735 AC: 111789 AN: 152100 Hom.: 41807 Cov.: 33 AF XY: 0.737 AC XY: 54791 AN XY: 74342

African (AFR) AF: 0.885 AC: 36770 AN: 41526

American (AMR) AF: 0.647 AC: 9854 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2135 AN: 3470

East Asian (EAS) AF: 0.656 AC: 3396 AN: 5176

South Asian (SAS) AF: 0.730 AC: 3520 AN: 4824

European-Finnish (FIN) AF: 0.723 AC: 7651 AN: 10580

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 46048 AN: 67970

Other (OTH) AF: 0.711 AC: 1501 AN: 2110

Alfa AF: 0.718 Hom.: 5165

Bravo AF: 0.735

Asia WGS AF: 0.727 AC: 2526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.55
DANN	Benign	0.17
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1975743; hg19: chr18-1690051;