1-119013136-C-T

Variant names:

• chr1-119013136-C-T
• rs1325933

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.79 in 151,988 control chromosomes in the GnomAD database, including 47,773 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 0.79 (47773 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.851 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: 0.790 AC: 119913 AN: 151870 Hom.: 47717 Cov.: 30

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.790 AC: 120023 AN: 151988 Hom.: 47773 Cov.: 30 AF XY: 0.791 AC XY: 58748 AN XY: 74292

African (AFR) AF: 0.859 AC: 35604 AN: 41452

American (AMR) AF: 0.789 AC: 12036 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2086 AN: 3472

East Asian (EAS) AF: 0.862 AC: 4450 AN: 5160

South Asian (SAS) AF: 0.655 AC: 3150 AN: 4812

European-Finnish (FIN) AF: 0.877 AC: 9267 AN: 10570

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.750 AC: 50983 AN: 67946

Other (OTH) AF: 0.748 AC: 1582 AN: 2114

Alfa AF: 0.745 Hom.: 69027

Bravo AF: 0.785

Asia WGS AF: 0.777 AC: 2702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	4.6
DANN	Benign	0.80
PhyloP100		0.068

Splicing

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

Other links and lift over

dbSNP: rs1325933; hg19: chr1-119555759;