rs4377733

Positions:

• chr5-91280763-C-T

Variant summary

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

The ENST00000660900.2(ENSG00000286638):​n.535C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 152,318 control chromosomes in the GnomAD database, including 52,800 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 0.83 (52757 hom., cov: 33)
  • Exomes 𝑓: 0.94 (43 hom.)
• Consequence: ENSG00000286638 ENST00000660900.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940

Genes affected

ENSG00000234292 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.91280763C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000234292	ENST00000440769.3	n.380G>A		non_coding_transcript_exon_variant	1/1	6
ENSG00000286638	ENST00000660900.2	n.535C>T		non_coding_transcript_exon_variant	1/1
LUCAT1	ENST00000647807.1	n.463+32875G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.829 AC: 126072 AN: 152102 Hom.: 52747 Cov.: 33

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.894

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.839

GnomAD4 exome AF: 0.939 AC: 92 AN: 98 Hom.: 43 Cov.: 0 AF XY: 0.919 AC XY: 57 AN XY: 62

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.978

Gnomad4 NFE exome AF: 0.977

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.829 AC: 126128 AN: 152220 Hom.: 52757 Cov.: 33 AF XY: 0.826 AC XY: 61491 AN XY: 74422

Gnomad4 AFR AF: 0.793

Gnomad4 AMR AF: 0.759

Gnomad4 ASJ AF: 0.912

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.752

Gnomad4 FIN AF: 0.894

Gnomad4 NFE AF: 0.877

Gnomad4 OTH AF: 0.836

Alfa AF: 0.859 Hom.: 12105

Bravo AF: 0.816

Asia WGS AF: 0.667 AC: 2324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	6.7
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4377733; hg19: chr5-90576580;