rs12127588

Positions:

• chr1-198626376-G-A
• chr1-198626376-G-C
• chr1-198626376-G-T

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 0.0691 in 152,200 control chromosomes in the GnomAD database, including 476 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 0.069 (476 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

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 (EAS) allele frequency at 95% confidence interval = 0.145 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: 0.0692 AC: 10525 AN: 152082 Hom.: 478 Cov.: 32

Gnomad AFR AF: 0.0169

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0794

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0747

Gnomad OTH AF: 0.0687

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

GnomAD4 genome AF: 0.0691 AC: 10523 AN: 152200 Hom.: 476 Cov.: 32 AF XY: 0.0742 AC XY: 5517 AN XY: 74396

Gnomad4 AFR AF: 0.0169

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.0794

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.0747

Gnomad4 OTH AF: 0.0680

Alfa AF: 0.0724 Hom.: 564

Bravo AF: 0.0661

Asia WGS AF: 0.132 AC: 457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12127588; hg19: chr1-198595506;