rs1564606

Variant names:

• chr12-84303354-A-C
• rs1564606

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 0.31 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.397 AC: 16260 AN: 40988

American (AMR) AF: 0.324 AC: 4898 AN: 15136

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1310 AN: 3462

East Asian (EAS) AF: 0.104 AC: 529 AN: 5094

South Asian (SAS) AF: 0.235 AC: 1126 AN: 4784

European-Finnish (FIN) AF: 0.219 AC: 2301 AN: 10492

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19240 AN: 67704

Other (OTH) AF: 0.314 AC: 659 AN: 2096

Alfa AF: 0.290 Hom.: 3928

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
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1564606; hg19: chr12-84697133;