rs12120904

Variant names:

• chr1-169508804-T-C
• rs12120904

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0869 in 152,106 control chromosomes in the GnomAD database, including 764 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 0.087 (764 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.373

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 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: 0.0869 AC: 13210 AN: 151988 Hom.: 763 Cov.: 32

Gnomad AFR AF: 0.0418

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0619

Gnomad ASJ AF: 0.0980

Gnomad EAS AF: 0.0402

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0849

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

GnomAD4 genome AF: 0.0869 AC: 13217 AN: 152106 Hom.: 764 Cov.: 32 AF XY: 0.0884 AC XY: 6576 AN XY: 74384

Gnomad4 AFR AF: 0.0418

Gnomad4 AMR AF: 0.0618

Gnomad4 ASJ AF: 0.0980

Gnomad4 EAS AF: 0.0399

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.0836

Alfa AF: 0.104 Hom.: 1172

Bravo AF: 0.0782

Asia WGS AF: 0.0660 AC: 230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.6
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12120904; hg19: chr1-169478042;