chr19-4086809-A-G

Variant names:

• chr19-4086809-A-G
• rs350818

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 0.773 in 151,972 control chromosomes in the GnomAD database, including 45,407 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 0.77 (45407 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 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: 0.773 AC: 117339 AN: 151854 Hom.: 45383 Cov.: 31

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.773 AC: 117408 AN: 151972 Hom.: 45407 Cov.: 31 AF XY: 0.775 AC XY: 57537 AN XY: 74248

Gnomad4 AFR AF: 0.740

Gnomad4 AMR AF: 0.812

Gnomad4 ASJ AF: 0.755

Gnomad4 EAS AF: 0.934

Gnomad4 SAS AF: 0.744

Gnomad4 FIN AF: 0.807

Gnomad4 NFE AF: 0.771

Gnomad4 OTH AF: 0.747

Alfa AF: 0.761 Hom.: 16982

Bravo AF: 0.772

Asia WGS AF: 0.821 AC: 2853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs350818; hg19: chr19-4086807;