1-119778464-G-A

Variant names:

• chr1-119778464-G-A
• rs12132674

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 0.229 in 152,024 control chromosomes in the GnomAD database, including 4,266 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 0.23 (4266 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34811 AN: 151908 Hom.: 4262 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.0405

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.229 AC: 34831 AN: 152024 Hom.: 4266 Cov.: 32 AF XY: 0.223 AC XY: 16579 AN XY: 74300

African (AFR) AF: 0.181 AC: 7507 AN: 41488

American (AMR) AF: 0.164 AC: 2514 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 824 AN: 3468

East Asian (EAS) AF: 0.0406 AC: 211 AN: 5192

South Asian (SAS) AF: 0.201 AC: 966 AN: 4806

European-Finnish (FIN) AF: 0.251 AC: 2644 AN: 10530

Middle Eastern (MID) AF: 0.202 AC: 59 AN: 292

European-Non Finnish (NFE) AF: 0.286 AC: 19412 AN: 67932

Other (OTH) AF: 0.208 AC: 439 AN: 2110

Alfa AF: 0.258 Hom.: 666

Bravo AF: 0.218

Asia WGS AF: 0.152 AC: 529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.36
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs12132674; hg19: chr1-120321087;