rs4808564

chr19-14853283-C-A

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 0.0651 in 152,118 control chromosomes in the GnomAD database, including 372 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 0.065 (372 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.294

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.117 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: 0.0652 AC: 9903 AN: 152000 Hom.: 373 Cov.: 32

Gnomad AFR AF: 0.0684

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0640

Gnomad ASJ AF: 0.0320

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.0403

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0620

Gnomad OTH AF: 0.0679

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

GnomAD4 genome AF: 0.0651 AC: 9900 AN: 152118 Hom.: 372 Cov.: 32 AF XY: 0.0662 AC XY: 4922 AN XY: 74366

Gnomad4 AFR AF: 0.0683

Gnomad4 AMR AF: 0.0640

Gnomad4 ASJ AF: 0.0320

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.0403

Gnomad4 NFE AF: 0.0620

Gnomad4 OTH AF: 0.0672

Alfa AF: 0.0622 Hom.: 314

Bravo AF: 0.0650

Asia WGS AF: 0.109 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.8
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4808564; hg19: chr19-14964095;