19-46431955-A-G

Variant names:

• chr19-46431955-A-G
• rs393760

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 0.819 in 152,142 control chromosomes in the GnomAD database, including 51,455 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 0.82 (51455 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.819 AC: 124470 AN: 152022 Hom.: 51402 Cov.: 31

Gnomad AFR AF: 0.928

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.817

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

GnomAD4 genome AF: 0.819 AC: 124582 AN: 152142 Hom.: 51455 Cov.: 31 AF XY: 0.820 AC XY: 60962 AN XY: 74340

African (AFR) AF: 0.928 AC: 38537 AN: 41532

American (AMR) AF: 0.819 AC: 12515 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.801 AC: 2778 AN: 3470

East Asian (EAS) AF: 0.858 AC: 4423 AN: 5156

South Asian (SAS) AF: 0.825 AC: 3984 AN: 4830

European-Finnish (FIN) AF: 0.775 AC: 8190 AN: 10574

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.757 AC: 51479 AN: 67988

Other (OTH) AF: 0.817 AC: 1728 AN: 2116

Alfa AF: 0.803 Hom.: 7464

Bravo AF: 0.825

Asia WGS AF: 0.828 AC: 2880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.0
DANN	Benign	0.62
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs393760; hg19: chr19-46935212;