rs103294

Variant names:

• chr19-54293995-T-C
• rs103294
• ENST00000417373.1:n.*54A>G

Variant summary

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

The ENST00000417373.1(ENSG00000240197):​n.*54A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 610,954 control chromosomes in the GnomAD database, including 191,790 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 0.81 (51083 hom., cov: 30)
  • Exomes 𝑓: 0.77 (140707 hom.)
• Consequence: ENSG00000240197 ENST00000417373.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254

Genes affected

ENSG00000240197 (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 (AFR) allele frequency at 95% confidence interval = 0.903 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
ENSG00000240197	ENST00000417373.1	n.*54A>G		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.813 AC: 123601 AN: 151970 Hom.: 51032 Cov.: 30

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.889

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.841

GnomAD4 exome AF: 0.772 AC: 354415 AN: 458866 Hom.: 140707 Cov.: 6 AF XY: 0.780 AC XY: 189621 AN XY: 243102

Gnomad4 AFR exome AF: 0.913

Gnomad4 AMR exome AF: 0.700

Gnomad4 ASJ exome AF: 0.919

Gnomad4 EAS exome AF: 0.328

Gnomad4 SAS exome AF: 0.851

Gnomad4 FIN exome AF: 0.714

Gnomad4 NFE exome AF: 0.796

Gnomad4 OTH exome AF: 0.802

GnomAD4 genome AF: 0.813 AC: 123714 AN: 152088 Hom.: 51083 Cov.: 30 AF XY: 0.808 AC XY: 60057 AN XY: 74370

Gnomad4 AFR AF: 0.911

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.917

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.838

Gnomad4 FIN AF: 0.706

Gnomad4 NFE AF: 0.796

Gnomad4 OTH AF: 0.840

Alfa AF: 0.805 Hom.: 72787

Bravo AF: 0.814

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs103294; hg19: chr19-54797848;