rs1564606

Positions:

• chr12-84303354-A-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 0.31 in 150,956 control chromosomes in the GnomAD database, including 7,578 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 0.31 (7578 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.392 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: 0.310 AC: 46790 AN: 150844 Hom.: 7569 Cov.: 31

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.310 AC: 46843 AN: 150956 Hom.: 7578 Cov.: 31 AF XY: 0.307 AC XY: 22610 AN XY: 73756

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.314

Alfa AF: 0.288 Hom.: 3533

Bravo AF: 0.320

Asia WGS AF: 0.185 AC: 644 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.51
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1564606; hg19: chr12-84697133;