rs11157990

Variant names:

• chr14-53917227-T-C
• rs11157990
• ENST00000426913.1:n.*43A>G

Variant summary

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

The ENST00000426913.1(ENSG00000231922):​n.*43A>G 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: ENSG00000231922 ENST00000426913.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.872

Genes affected

ENSG00000231922 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231922	ENST00000426913.1	n.*43A>G		downstream_gene_variant		6

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;