rs1446969

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000289484 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000289484	ENST00000733167.1	n.672+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

African (AFR) AF: 0.678 AC: 28080 AN: 41402

American (AMR) AF: 0.895 AC: 13692 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.921 AC: 3196 AN: 3472

East Asian (EAS) AF: 0.986 AC: 5075 AN: 5148

South Asian (SAS) AF: 0.894 AC: 4311 AN: 4820

European-Finnish (FIN) AF: 0.852 AC: 9020 AN: 10584

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.876 AC: 59570 AN: 67996

Other (OTH) AF: 0.853 AC: 1791 AN: 2100

Alfa AF: 0.859 Hom.: 16375

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
PhyloP100		-0.031

Splicing

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

Other links and lift over

dbSNP: rs1446969; hg19: chr1-159548879;