rs11157990

chr14-53917227-T-C

Variant summary

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

The 14-53917227-T-C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,094 control chromosomes in the GnomAD database, including 4,714 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 0.24 (4714 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENST00000426913.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.872

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.293 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
	ENST00000426913.1			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35812 AN: 151972 Hom.: 4719 Cov.: 33

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.251

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 FIN exome AF: 0.00

GnomAD4 genome AF: 0.235 AC: 35795 AN: 152094 Hom.: 4714 Cov.: 33 AF XY: 0.236 AC XY: 17535 AN XY: 74352

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.248

Alfa AF: 0.265 Hom.: 3074

Bravo AF: 0.227

Asia WGS AF: 0.229 AC: 796 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.1
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11157990; hg19: chr14-54383945;