rs4808260

chr19-20663465-C-G

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 0.715 in 151,796 control chromosomes in the GnomAD database, including 39,120 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 0.71 (39120 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.869

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.742 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: 0.715 AC: 108453 AN: 151680 Hom.: 39094 Cov.: 30

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.715 AC: 108524 AN: 151796 Hom.: 39120 Cov.: 30 AF XY: 0.715 AC XY: 53020 AN XY: 74130

Gnomad4 AFR AF: 0.672

Gnomad4 AMR AF: 0.656

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.584

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.796

Gnomad4 NFE AF: 0.748

Gnomad4 OTH AF: 0.723

Alfa AF: 0.734 Hom.: 5110

Bravo AF: 0.701

Asia WGS AF: 0.628 AC: 2185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.3
Dann	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4808260; hg19: chr19-20846271;