rs12063072

Positions:

• chr1-156143270-G-A
• chr1-156143270-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 0.0748 in 151,330 control chromosomes in the GnomAD database, including 870 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 0.075 (870 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.188 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: 0.0748 AC: 11313 AN: 151214 Hom.: 870 Cov.: 30

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.0606

Gnomad AMR AF: 0.0318

Gnomad ASJ AF: 0.0396

Gnomad EAS AF: 0.0221

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0266

Gnomad MID AF: 0.0350

Gnomad NFE AF: 0.0260

Gnomad OTH AF: 0.0543

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

GnomAD4 genome AF: 0.0748 AC: 11325 AN: 151330 Hom.: 870 Cov.: 30 AF XY: 0.0732 AC XY: 5407 AN XY: 73872

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.0318

Gnomad4 ASJ AF: 0.0396

Gnomad4 EAS AF: 0.0219

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.0266

Gnomad4 NFE AF: 0.0259

Gnomad4 OTH AF: 0.0542

Alfa AF: 0.0322 Hom.: 73

Bravo AF: 0.0774

Asia WGS AF: 0.0650 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.0
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12063072; hg19: chr1-156113061;