rs12128121

Variant names:

• chr1-22605669-A-G
• rs12128121

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 0.0967 in 152,270 control chromosomes in the GnomAD database, including 851 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 0.097 (851 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.60

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.173 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: 0.0966 AC: 14694 AN: 152152 Hom.: 846 Cov.: 32

Gnomad AFR AF: 0.0484

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.0971

Gnomad EAS AF: 0.0543

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0949

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.0967 AC: 14722 AN: 152270 Hom.: 851 Cov.: 32 AF XY: 0.0995 AC XY: 7407 AN XY: 74450

Gnomad4 AFR AF: 0.0488

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.0971

Gnomad4 EAS AF: 0.0542

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.0949

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.108

Alfa AF: 0.116 Hom.: 1072

Bravo AF: 0.102

Asia WGS AF: 0.115 AC: 400 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12128121; hg19: chr1-22932162;