rs2386592

Variant names:

• chr5-10174546-A-G
• rs2386592

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 0.355 in 152,150 control chromosomes in the GnomAD database, including 10,465 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 0.36 (10465 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.807

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.438 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: 0.356 AC: 54055 AN: 152030 Hom.: 10463 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.355 AC: 54081 AN: 152150 Hom.: 10465 Cov.: 32 AF XY: 0.352 AC XY: 26211 AN XY: 74374

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.362

Alfa AF: 0.376 Hom.: 1429

Bravo AF: 0.356

Asia WGS AF: 0.230 AC: 804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.3
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2386592; hg19: chr5-10174658;