19-46792395-A-G

Variant names:

• chr19-46792395-A-G
• rs918486

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0680 AC: 2822 AN: 41526

American (AMR) AF: 0.0860 AC: 1313 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0568 AC: 197 AN: 3470

East Asian (EAS) AF: 0.218 AC: 1128 AN: 5172

South Asian (SAS) AF: 0.153 AC: 738 AN: 4814

European-Finnish (FIN) AF: 0.0347 AC: 369 AN: 10624

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0349 AC: 2373 AN: 68012

Other (OTH) AF: 0.0626 AC: 132 AN: 2110

Alfa AF: 0.0472 Hom.: 127

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
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs918486; hg19: chr19-47295652;