rs1384936

Variant names:

• chr19-5423632-C-T
• rs1384936

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 0.581 in 151,828 control chromosomes in the GnomAD database, including 25,892 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 0.58 (25892 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.64 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: 0.581 AC: 88206 AN: 151710 Hom.: 25872 Cov.: 30

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.581 AC: 88275 AN: 151828 Hom.: 25892 Cov.: 30 AF XY: 0.583 AC XY: 43266 AN XY: 74186

African (AFR) AF: 0.496 AC: 20526 AN: 41368

American (AMR) AF: 0.635 AC: 9678 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2204 AN: 3468

East Asian (EAS) AF: 0.658 AC: 3401 AN: 5166

South Asian (SAS) AF: 0.572 AC: 2757 AN: 4820

European-Finnish (FIN) AF: 0.627 AC: 6601 AN: 10534

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.606 AC: 41149 AN: 67924

Other (OTH) AF: 0.591 AC: 1245 AN: 2106

Alfa AF: 0.601 Hom.: 82797

Bravo AF: 0.581

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.33
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1384936; hg19: chr19-5423643;