rs561779

Variant names:

• chr4-46236761-A-G
• rs561779

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 0.625 in 151,750 control chromosomes in the GnomAD database, including 30,241 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 0.62 (30241 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17

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 (SAS) allele frequency at 95% confidence interval = 0.757 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: 0.625 AC: 94776 AN: 151632 Hom.: 30220 Cov.: 32

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.777

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.625 AC: 94838 AN: 151750 Hom.: 30241 Cov.: 32 AF XY: 0.626 AC XY: 46361 AN XY: 74098

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.695

Gnomad4 EAS AF: 0.544

Gnomad4 SAS AF: 0.778

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.570

Gnomad4 OTH AF: 0.626

Alfa AF: 0.587 Hom.: 4564

Bravo AF: 0.620

Asia WGS AF: 0.648 AC: 2253 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs561779; hg19: chr4-46238778;