rs1020382

Variant names:

• chr19-267039-C-T
• rs1020382

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.838

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.713

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.634

Alfa AF: 0.597 Hom.: 36674

Bravo AF: 0.642

Asia WGS AF: 0.374 AC: 1302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1020382; hg19: chr19-267039;