chr10-5020020-G-A

Variant names:

• chr10-5020020-G-A
• rs1937883

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 0.235 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.112 AC: 4656 AN: 41506

American (AMR) AF: 0.267 AC: 4077 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1008 AN: 3470

East Asian (EAS) AF: 0.0493 AC: 255 AN: 5176

South Asian (SAS) AF: 0.265 AC: 1276 AN: 4816

European-Finnish (FIN) AF: 0.287 AC: 3031 AN: 10550

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20468 AN: 67942

Other (OTH) AF: 0.235 AC: 493 AN: 2098

Alfa AF: 0.260 Hom.: 2028

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
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs1937883; hg19: chr10-5062212;