rs12127588

Variant names:

• chr1-198626376-G-A
• rs12127588

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;