rs12120904

Positions:

• chr1-169508804-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;