rs1020382

Variant names:

• chr19-267039-C-T
• rs1020382

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 0.638 in 152,176 control chromosomes in the GnomAD database, including 32,865 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 0.64 (32865 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.83 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: 0.638 AC: 97047 AN: 152058 Hom.: 32823 Cov.: 33

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.638 AC: 97137 AN: 152176 Hom.: 32865 Cov.: 33 AF XY: 0.632 AC XY: 47020 AN XY: 74398

African (AFR) AF: 0.838 AC: 34791 AN: 41532

American (AMR) AF: 0.535 AC: 8188 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2470 AN: 3464

East Asian (EAS) AF: 0.139 AC: 716 AN: 5162

South Asian (SAS) AF: 0.473 AC: 2275 AN: 4814

European-Finnish (FIN) AF: 0.636 AC: 6737 AN: 10590

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39775 AN: 68000

Other (OTH) AF: 0.634 AC: 1340 AN: 2114

Alfa AF: 0.602 Hom.: 51998

Bravo AF: 0.642

Asia WGS AF: 0.374 AC: 1302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.3
DANN	Benign	0.53
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1020382; hg19: chr19-267039;