1-119494155-C-T

Variant names:

• chr1-119494155-C-T
• rs1856888

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 0.674 in 152,180 control chromosomes in the GnomAD database, including 34,769 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 0.67 (34769 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.563

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 = 0.859 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

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102450 AN: 152062 Hom.: 34750 Cov.: 33

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.674 AC: 102519 AN: 152180 Hom.: 34769 Cov.: 33 AF XY: 0.683 AC XY: 50806 AN XY: 74388

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.736

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.880

Gnomad4 SAS AF: 0.781

Gnomad4 FIN AF: 0.737

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.660

Alfa AF: 0.569 Hom.: 1652

Bravo AF: 0.670

Asia WGS AF: 0.784 AC: 2727 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	0.84
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1856888; hg19: chr1-120036778; COSMIC: COSV70872645;