1-159579089-C-T

Position:

• chr1-159579089-C-T

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, non coding transcript 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: ENST00000693113.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000693113.1	n.652+1757G>A		intron_variant, non_coding_transcript_variant

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;