1-16514091-C-T

Position:

• chr1-16514091-C-T

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 0.398 in 144,778 control chromosomes in the GnomAD database, including 10,224 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 0.40 (10224 hom., cov: 34)
  • Exomes 𝑓: 0.22 (11 hom.)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.16514091C>T		intergenic_region
RNU1-1	NR_004430.2	n.*31G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RNU1-1	ENST00000383925.1	n.*31G>A		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.399 AC: 57668 AN: 144660 Hom.: 10226 Cov.: 34

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.447

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.418

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.216 AC: 257 AN: 1188 Hom.: 11 Cov.: 0 AF XY: 0.218 AC XY: 128 AN XY: 586

Gnomad4 AFR exome AF: 0.0469

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.224

Gnomad4 OTH exome AF: 0.286

GnomAD4 genome AF: 0.398 AC: 57667 AN: 144778 Hom.: 10224 Cov.: 34 AF XY: 0.405 AC XY: 28579 AN XY: 70644

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.711

Gnomad4 SAS AF: 0.529

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.416

Alfa AF: 0.207 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.064
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs157253; hg19: chr1-16840586;