rs12119648

Variant names:

• chr1-223512092-G-A
• rs12119648

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 0.373 in 151,670 control chromosomes in the GnomAD database, including 11,846 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 0.37 (11846 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.669
• Publications: 0 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 (EAS) allele frequency at 95% confidence interval = 0.505 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: 0.373 AC: 56604 AN: 151552 Hom.: 11861 Cov.: 29

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.373 AC: 56602 AN: 151670 Hom.: 11846 Cov.: 29 AF XY: 0.375 AC XY: 27762 AN XY: 74124

African (AFR) AF: 0.161 AC: 6662 AN: 41360

American (AMR) AF: 0.446 AC: 6799 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1608 AN: 3468

East Asian (EAS) AF: 0.522 AC: 2672 AN: 5120

South Asian (SAS) AF: 0.432 AC: 2064 AN: 4776

European-Finnish (FIN) AF: 0.405 AC: 4265 AN: 10522

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31061 AN: 67882

Other (OTH) AF: 0.400 AC: 842 AN: 2106

Alfa AF: 0.410 Hom.: 1688

Bravo AF: 0.369

Asia WGS AF: 0.439 AC: 1528 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.65
DANN	Benign	0.68
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs12119648; hg19: chr1-223685434;