rs12130862

Variant names:

• chr1-152054539-A-T
• rs12130862

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 0.145 in 152,248 control chromosomes in the GnomAD database, including 2,245 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 0.15 (2245 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.70

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 = 0.206 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: 0.146 AC: 22155 AN: 152130 Hom.: 2243 Cov.: 32

Gnomad AFR AF: 0.0409

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.145 AC: 22147 AN: 152248 Hom.: 2245 Cov.: 32 AF XY: 0.147 AC XY: 10927 AN XY: 74438

Gnomad4 AFR AF: 0.0408

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.148

Alfa AF: 0.190 Hom.: 397

Bravo AF: 0.125

Asia WGS AF: 0.0590 AC: 207 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.8
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12130862; hg19: chr1-152027015;