ENST00000646678.1:n.-103C>T

Variant names:

• chr1-84038426-C-T
• rs566830
• ENST00000646678.1:n.-103C>T

Variant summary

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

The ENST00000646678.1(ENSG00000285201):​n.-103C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 152,206 control chromosomes in the GnomAD database, including 49,233 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 0.80 (49220 hom., cov: 32)
  • Exomes 𝑓: 0.82 (13 hom.)
• Consequence: ENSG00000285201 ENST00000646678.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

Genes affected

ENSG00000285201 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.888 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
ENSG00000285201	ENST00000646678.1	n.-103C>T		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121765 AN: 152048 Hom.: 49184 Cov.: 32

Gnomad AFR AF: 0.895

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.813

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.788

GnomAD4 exome AF: 0.825 AC: 33 AN: 40 Hom.: 13 AF XY: 0.813 AC XY: 26 AN XY: 32

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.821

GnomAD4 genome AF: 0.801 AC: 121846 AN: 152166 Hom.: 49220 Cov.: 32 AF XY: 0.803 AC XY: 59700 AN XY: 74376

Gnomad4 AFR AF: 0.895

Gnomad4 AMR AF: 0.812

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.900

Gnomad4 SAS AF: 0.753

Gnomad4 FIN AF: 0.773

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.778

Alfa AF: 0.770 Hom.: 5612

Bravo AF: 0.810

Asia WGS AF: 0.787 AC: 2736 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	1.1
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs566830; hg19: chr1-84504109; COSMIC: COSV59966700;