chr19-46792395-A-G

Position:

• chr19-46792395-A-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 0.0604 in 152,200 control chromosomes in the GnomAD database, including 425 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 0.060 (425 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.46792395A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0604 AC: 9181 AN: 152082 Hom.: 420 Cov.: 31

Gnomad AFR AF: 0.0680

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.0854

Gnomad ASJ AF: 0.0568

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0347

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0349

Gnomad OTH AF: 0.0594

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

GnomAD4 genome AF: 0.0604 AC: 9196 AN: 152200 Hom.: 425 Cov.: 31 AF XY: 0.0620 AC XY: 4611 AN XY: 74416

Gnomad4 AFR AF: 0.0680

Gnomad4 AMR AF: 0.0860

Gnomad4 ASJ AF: 0.0568

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.0347

Gnomad4 NFE AF: 0.0349

Gnomad4 OTH AF: 0.0626

Alfa AF: 0.0481 Hom.: 118

Bravo AF: 0.0660

Asia WGS AF: 0.187 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.4
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs918486; hg19: chr19-47295652;