rs12119367

Variant names:

• chr1-233602658-A-C
• rs12119367

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 0.14 in 152,252 control chromosomes in the GnomAD database, including 1,758 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 0.14 (1758 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21362 AN: 152134 Hom.: 1758 Cov.: 33

Gnomad AFR AF: 0.0590

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.0979

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.140 AC: 21373 AN: 152252 Hom.: 1758 Cov.: 33 AF XY: 0.139 AC XY: 10335 AN XY: 74442

African (AFR) AF: 0.0589 AC: 2446 AN: 41550

American (AMR) AF: 0.199 AC: 3048 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 857 AN: 3466

East Asian (EAS) AF: 0.0979 AC: 508 AN: 5188

South Asian (SAS) AF: 0.184 AC: 885 AN: 4820

European-Finnish (FIN) AF: 0.138 AC: 1459 AN: 10592

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11611 AN: 68036

Other (OTH) AF: 0.148 AC: 313 AN: 2110

Alfa AF: 0.162 Hom.: 4579

Bravo AF: 0.144

Asia WGS AF: 0.156 AC: 547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.74
DANN	Benign	0.46
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs12119367; hg19: chr1-233738404;