rs12128121

Positions:

• chr1-22605669-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;