rs564367

Variant names:

• chr1-60653259-A-G
• rs564367

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 0.47 in 151,996 control chromosomes in the GnomAD database, including 16,923 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 0.47 (16923 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.617 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: 0.470 AC: 71353 AN: 151878 Hom.: 16909 Cov.: 32

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.470 AC: 71387 AN: 151996 Hom.: 16923 Cov.: 32 AF XY: 0.471 AC XY: 34956 AN XY: 74272

African (AFR) AF: 0.461 AC: 19099 AN: 41456

American (AMR) AF: 0.504 AC: 7697 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1659 AN: 3468

East Asian (EAS) AF: 0.635 AC: 3273 AN: 5152

South Asian (SAS) AF: 0.581 AC: 2790 AN: 4806

European-Finnish (FIN) AF: 0.409 AC: 4320 AN: 10560

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.455 AC: 30928 AN: 67986

Other (OTH) AF: 0.493 AC: 1038 AN: 2104

Alfa AF: 0.461 Hom.: 3943

Bravo AF: 0.475

Asia WGS AF: 0.595 AC: 2068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.6
DANN	Benign	0.74
PhyloP100		0.051

Splicing

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

Other links and lift over

dbSNP: rs564367; hg19: chr1-61118931;