rs1567757

Variant names:

• chr12-52688469-C-A
• rs1567757

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.456 AC: 18894 AN: 41466

American (AMR) AF: 0.423 AC: 6460 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1662 AN: 3466

East Asian (EAS) AF: 0.239 AC: 1233 AN: 5166

South Asian (SAS) AF: 0.474 AC: 2284 AN: 4814

European-Finnish (FIN) AF: 0.468 AC: 4933 AN: 10548

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32109 AN: 67950

Other (OTH) AF: 0.438 AC: 925 AN: 2112

Alfa AF: 0.466 Hom.: 64900

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
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs1567757; hg19: chr12-53082253;