rs4932217

chr15-89358801-A-Cchr15-89358801-A-Gchr15-89358801-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The 15-89358801-A-C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 152,212 control chromosomes in the GnomAD database, including 23,697 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 0.53 (23691 hom., cov: 33)
  • Exomes 𝑓: 0.36 (6 hom.)
• Consequence: ENST00000624115.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.473

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000624115.1			upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80150 AN: 152000 Hom.: 23648 Cov.: 33

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.493

GnomAD4 exome AF: 0.362 AC: 34 AN: 94 Hom.: 6 Cov.: 0 AF XY: 0.353 AC XY: 24 AN XY: 68

Gnomad4 FIN exome AF: 0.400

Gnomad4 NFE exome AF: 0.344

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.527 AC: 80238 AN: 152118 Hom.: 23691 Cov.: 33 AF XY: 0.528 AC XY: 39270 AN XY: 74376

Gnomad4 AFR AF: 0.806

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.482

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.487

Alfa AF: 0.418 Hom.: 17639

Bravo AF: 0.538

Asia WGS AF: 0.408 AC: 1417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	7.1
Dann	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4932217; hg19: chr15-89902032;