chr19-18374112-G-T

Variant names:

• chr19-18374112-G-T
• rs888663

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 0.836 in 152,078 control chromosomes in the GnomAD database, including 53,320 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 0.84 (53320 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.46
• Publications: 33 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127014 AN: 151960 Hom.: 53272 Cov.: 31

Gnomad AFR AF: 0.892

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.881

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.814

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

GnomAD4 genome AF: 0.836 AC: 127118 AN: 152078 Hom.: 53320 Cov.: 31 AF XY: 0.837 AC XY: 62160 AN XY: 74306

African (AFR) AF: 0.892 AC: 37016 AN: 41506

American (AMR) AF: 0.834 AC: 12717 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.849 AC: 2945 AN: 3470

East Asian (EAS) AF: 0.819 AC: 4226 AN: 5160

South Asian (SAS) AF: 0.731 AC: 3525 AN: 4824

European-Finnish (FIN) AF: 0.881 AC: 9330 AN: 10594

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.804 AC: 54673 AN: 67964

Other (OTH) AF: 0.808 AC: 1703 AN: 2108

Alfa AF: 0.812 Hom.: 150215

Bravo AF: 0.837

Asia WGS AF: 0.760 AC: 2644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.079
DANN	Benign	0.67
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs888663; hg19: chr19-18484922;