rs1567757

Variant names:

• chr12-52688469-C-A
• rs1567757

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 0.456 in 151,988 control chromosomes in the GnomAD database, including 16,005 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 0.46 (16005 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214

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 (SAS) allele frequency at 95% confidence interval = 0.468 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: 0.456 AC: 69223 AN: 151870 Hom.: 15966 Cov.: 32

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.456 AC: 69307 AN: 151988 Hom.: 16005 Cov.: 32 AF XY: 0.452 AC XY: 33560 AN XY: 74270

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.423

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.438

Alfa AF: 0.467 Hom.: 28458

Bravo AF: 0.450

Asia WGS AF: 0.426 AC: 1480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1567757; hg19: chr12-53082253;