rs12756570

chr1-158391311-C-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 0.0603 in 152,142 control chromosomes in the GnomAD database, including 408 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 0.060 (408 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.602

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0876 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: 0.0603 AC: 9173 AN: 152024 Hom.: 407 Cov.: 32

Gnomad AFR AF: 0.0203

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.0412

Gnomad ASJ AF: 0.0484

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0419

Gnomad FIN AF: 0.0987

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0895

Gnomad OTH AF: 0.0605

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

GnomAD4 genome AF: 0.0603 AC: 9173 AN: 152142 Hom.: 408 Cov.: 32 AF XY: 0.0599 AC XY: 4458 AN XY: 74382

Gnomad4 AFR AF: 0.0204

Gnomad4 AMR AF: 0.0411

Gnomad4 ASJ AF: 0.0484

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0423

Gnomad4 FIN AF: 0.0987

Gnomad4 NFE AF: 0.0895

Gnomad4 OTH AF: 0.0598

Alfa AF: 0.0781 Hom.: 645

Bravo AF: 0.0529

Asia WGS AF: 0.0170 AC: 61 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.44
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12756570; hg19: chr1-158361101;