rs103294

Positions:

• chr19-54293995-T-C

Variant summary

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

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254

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 (AFR) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.54293995T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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;