rs2386592

Variant names:

• chr5-10174546-A-G
• rs2386592

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 0.355 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.208 AC: 8620 AN: 41538

American (AMR) AF: 0.447 AC: 6840 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1502 AN: 3468

East Asian (EAS) AF: 0.137 AC: 710 AN: 5186

South Asian (SAS) AF: 0.351 AC: 1693 AN: 4822

European-Finnish (FIN) AF: 0.401 AC: 4232 AN: 10552

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29143 AN: 67974

Other (OTH) AF: 0.362 AC: 765 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.3
DANN	Benign	0.68
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs2386592; hg19: chr5-10174658;