rs10039217

Variant names:

• chr5-175751872-A-G
• rs10039217

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 0.0446 in 152,298 control chromosomes in the GnomAD database, including 279 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 0.045 (279 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.546

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.108 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: 0.0446 AC: 6785 AN: 152180 Hom.: 279 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0186

Gnomad ASJ AF: 0.0464

Gnomad EAS AF: 0.0287

Gnomad SAS AF: 0.0425

Gnomad FIN AF: 0.0142

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0171

Gnomad OTH AF: 0.0401

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

GnomAD4 genome AF: 0.0446 AC: 6796 AN: 152298 Hom.: 279 Cov.: 32 AF XY: 0.0436 AC XY: 3245 AN XY: 74474

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.0186

Gnomad4 ASJ AF: 0.0464

Gnomad4 EAS AF: 0.0286

Gnomad4 SAS AF: 0.0429

Gnomad4 FIN AF: 0.0142

Gnomad4 NFE AF: 0.0171

Gnomad4 OTH AF: 0.0392

Alfa AF: 0.0292 Hom.: 47

Bravo AF: 0.0472

Asia WGS AF: 0.0360 AC: 127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10039217; hg19: chr5-175178875;