18-1690050-C-T

Variant summary

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

The ENST00000580524.1(ENSG00000266450):n.408+33555C>T variant causes a intron, non coding transcript 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: ENST00000580524.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000580524.1	n.408+33555C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000661994.1	n.374+40257C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.885

Gnomad4 AMR AF: 0.647

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.656

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.723

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.711

Alfa AF: 0.711 Hom.: 4858

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1975743; hg19: chr18-1690051;