rs12088543

chr1-84252300-T-C

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 0.132 in 152,016 control chromosomes in the GnomAD database, including 2,157 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 0.13 (2157 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.133

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.343 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: 0.132 AC: 20082 AN: 151898 Hom.: 2153 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.0210

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0363

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.132 AC: 20105 AN: 152016 Hom.: 2157 Cov.: 32 AF XY: 0.139 AC XY: 10311 AN XY: 74274

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.0210

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.0363

Gnomad4 OTH AF: 0.119

Alfa AF: 0.0726 Hom.: 756

Bravo AF: 0.145

Asia WGS AF: 0.260 AC: 900 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	5.0
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12088543; hg19: chr1-84717983;