1-159705927-T-C

Position:

• chr1-159705927-T-C

Variant summary

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

The variant allele was found at a frequency of 0.835 in 152,100 control chromosomes in the GnomAD database, including 53,159 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 (53159 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.159705927T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126828 AN: 151982 Hom.: 53104 Cov.: 30

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.830

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.835 AC: 126946 AN: 152100 Hom.: 53159 Cov.: 30 AF XY: 0.836 AC XY: 62130 AN XY: 74346

Gnomad4 AFR AF: 0.870

Gnomad4 AMR AF: 0.881

Gnomad4 ASJ AF: 0.842

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.783

Gnomad4 FIN AF: 0.830

Gnomad4 NFE AF: 0.793

Gnomad4 OTH AF: 0.845

Alfa AF: 0.816 Hom.: 12232

Bravo AF: 0.841

Asia WGS AF: 0.868 AC: 3018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.16
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs876538; hg19: chr1-159675717;