rs1446969

Variant names:

• chr1-159579089-C-T
• rs1446969
• ENST00000693113.1:n.652+1757G>A

Variant summary

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

The ENST00000693113.1(ENSG00000289484):​n.652+1757G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.828 in 152,018 control chromosomes in the GnomAD database, including 52,781 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 (52781 hom., cov: 30)
• Consequence: ENSG00000289484 ENST00000693113.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310

Genes affected

ENSG00000289484 (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 (EAS) allele frequency at 95% confidence interval = 0.963 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
ENSG00000289484	ENST00000693113.1	n.652+1757G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.828 AC: 125737 AN: 151900 Hom.: 52755 Cov.: 30

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.895

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.852

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

GnomAD4 genome AF: 0.828 AC: 125806 AN: 152018 Hom.: 52781 Cov.: 30 AF XY: 0.828 AC XY: 61529 AN XY: 74310

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.895

Gnomad4 ASJ AF: 0.921

Gnomad4 EAS AF: 0.986

Gnomad4 SAS AF: 0.894

Gnomad4 FIN AF: 0.852

Gnomad4 NFE AF: 0.876

Gnomad4 OTH AF: 0.853

Alfa AF: 0.845 Hom.: 6783

Bravo AF: 0.826

Asia WGS AF: 0.913 AC: 3175 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	0.88
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1446969; hg19: chr1-159548879;