10-5020020-G-A

Position:

• chr10-5020020-G-A

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 0.235 in 152,040 control chromosomes in the GnomAD database, including 4,741 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 0.23 (4741 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.421

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35669 AN: 151922 Hom.: 4744 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.0492

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.235 AC: 35672 AN: 152040 Hom.: 4741 Cov.: 32 AF XY: 0.235 AC XY: 17453 AN XY: 74316

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.0493

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.235

Alfa AF: 0.273 Hom.: 1197

Bravo AF: 0.227

Asia WGS AF: 0.179 AC: 623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.75
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1937883; hg19: chr10-5062212;