1-226348944-C-T

Variant names:

• chr1-226348944-C-T
• rs874583
• ENST00000690647.1:n.-227C>T

Variant summary

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

The ENST00000690647.1(ENSG00000289348):​n.-227C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 151,866 control chromosomes in the GnomAD database, including 29,959 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 0.62 (29959 hom., cov: 30)
• Consequence: ENSG00000289348 ENST00000690647.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

Genes affected

ENSG00000289348 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.883 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
ENSG00000289348	ENST00000690647.1	n.-227C>T		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94217 AN: 151748 Hom.: 29913 Cov.: 30

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.621 AC: 94321 AN: 151866 Hom.: 29959 Cov.: 30 AF XY: 0.625 AC XY: 46403 AN XY: 74204

Gnomad4 AFR AF: 0.698

Gnomad4 AMR AF: 0.615

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.905

Gnomad4 SAS AF: 0.651

Gnomad4 FIN AF: 0.646

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.619

Alfa AF: 0.566 Hom.: 31199

Bravo AF: 0.624

Asia WGS AF: 0.781 AC: 2715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.52
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs874583; hg19: chr1-226536645;