19-18152893-C-G

Variant names:

• chr19-18152893-C-G
• rs3736328

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 0.481 in 152,104 control chromosomes in the GnomAD database, including 18,253 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 0.48 (18253 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.56
• Publications: 10 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 = 0.723 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73220 AN: 151986 Hom.: 18255 Cov.: 33

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.481 AC: 73237 AN: 152104 Hom.: 18253 Cov.: 33 AF XY: 0.482 AC XY: 35837 AN XY: 74342

African (AFR) AF: 0.355 AC: 14729 AN: 41494

American (AMR) AF: 0.510 AC: 7800 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1654 AN: 3468

East Asian (EAS) AF: 0.742 AC: 3838 AN: 5170

South Asian (SAS) AF: 0.654 AC: 3155 AN: 4824

European-Finnish (FIN) AF: 0.482 AC: 5091 AN: 10566

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35171 AN: 67982

Other (OTH) AF: 0.476 AC: 1005 AN: 2112

Alfa AF: 0.487 Hom.: 2264

Bravo AF: 0.475

Asia WGS AF: 0.672 AC: 2334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.030
DANN	Benign	0.44
PhyloP100		-3.6
PromoterAI		-0.020	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3736328; hg19: chr19-18263703;