1-119812890-C-T

Variant names:

• chr1-119812890-C-T
• rs2994811

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 0.817 in 152,100 control chromosomes in the GnomAD database, including 51,276 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 0.82 (51276 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.460
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.893 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: 0.817 AC: 124192 AN: 151982 Hom.: 51227 Cov.: 31

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.817 AC: 124297 AN: 152100 Hom.: 51276 Cov.: 31 AF XY: 0.817 AC XY: 60734 AN XY: 74358

African (AFR) AF: 0.901 AC: 37388 AN: 41492

American (AMR) AF: 0.779 AC: 11904 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.826 AC: 2859 AN: 3462

East Asian (EAS) AF: 0.480 AC: 2481 AN: 5172

South Asian (SAS) AF: 0.839 AC: 4039 AN: 4814

European-Finnish (FIN) AF: 0.815 AC: 8616 AN: 10568

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.798 AC: 54254 AN: 67994

Other (OTH) AF: 0.821 AC: 1735 AN: 2112

Alfa AF: 0.810 Hom.: 36356

Bravo AF: 0.818

Asia WGS AF: 0.677 AC: 2357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.28
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs2994811; hg19: chr1-120355513;