rs4807000

chr19-4831866-A-Gchr19-4831866-A-T

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 0.667 in 151,838 control chromosomes in the GnomAD database, including 34,446 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 0.67 (34446 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.79 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: 0.667 AC: 101250 AN: 151720 Hom.: 34406 Cov.: 31

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.667 AC: 101350 AN: 151838 Hom.: 34446 Cov.: 31 AF XY: 0.669 AC XY: 49614 AN XY: 74210

Gnomad4 AFR AF: 0.797

Gnomad4 AMR AF: 0.653

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.595

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.624

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.650

Alfa AF: 0.633 Hom.: 3860

Bravo AF: 0.669

Asia WGS AF: 0.645 AC: 2244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.21
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4807000; hg19: chr19-4831878;