rs12030600

chr1-231469633-G-A

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 0.121 in 152,054 control chromosomes in the GnomAD database, including 1,704 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 0.12 (1704 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.492

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.433 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: 0.121 AC: 18338 AN: 151936 Hom.: 1696 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0795

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.0568

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0565

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.121 AC: 18363 AN: 152054 Hom.: 1704 Cov.: 32 AF XY: 0.125 AC XY: 9312 AN XY: 74338

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.0795

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.0568

Gnomad4 NFE AF: 0.0566

Gnomad4 OTH AF: 0.125

Alfa AF: 0.0832 Hom.: 219

Bravo AF: 0.127

Asia WGS AF: 0.315 AC: 1093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	3.8
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12030600; hg19: chr1-231605379;