rs564367

Variant names:

• chr1-60653259-A-G
• rs564367

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 0.47 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.635

Gnomad4 SAS AF: 0.581

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.493

Alfa AF: 0.461 Hom.: 3870

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs564367; hg19: chr1-61118931;