rs58532686

Variant names:

• chr16-55652904-CCT-C
• rs58532686
• XR_007065075.1:n.*200_*201delAG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The XR_007065075.1(LOC124903693):​n.*200_*201delAG variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0491 in 152,274 control chromosomes in the GnomAD database, including 348 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.049 (348 hom., cov: 32)
• Consequence: LOC124903693 XR_007065075.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.500
• Publications: 1 publications found

Genes affected

LOC124903693 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0490 AC: 7462 AN: 152156 Hom.: 348 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.00220

Gnomad AMR AF: 0.0237

Gnomad ASJ AF: 0.0392

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.00786

Gnomad FIN AF: 0.00376

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0219

Gnomad OTH AF: 0.0425

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

GnomAD4 genome AF: 0.0491 AC: 7473 AN: 152274 Hom.: 348 Cov.: 32 AF XY: 0.0471 AC XY: 3503 AN XY: 74444

African (AFR) AF: 0.128 AC: 5302 AN: 41518

American (AMR) AF: 0.0237 AC: 362 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0392 AC: 136 AN: 3472

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5168

South Asian (SAS) AF: 0.00766 AC: 37 AN: 4830

European-Finnish (FIN) AF: 0.00376 AC: 40 AN: 10626

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0219 AC: 1487 AN: 68036

Other (OTH) AF: 0.0425 AC: 90 AN: 2116

Alfa AF: 0.0358 Hom.: 28

Bravo AF: 0.0547

Asia WGS AF: 0.0160 AC: 56 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs58532686; hg19: chr16-55686816;