chr1-16514091-C-T

Variant names:

• chr1-16514091-C-T
• rs157253
• ENST00000383925.1:n.*31G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000383925.1(RNU1-1):​n.*31G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. 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: RNU1-1 ENST00000383925.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46
• Publications: 0 publications found

Genes affected

RNU1-1 (HGNC:10120): (RNA, U1 small nuclear 1)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000383925.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNU1-1	NR_004430.4		n.*31G>A		downstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNU1-1	ENST00000383925.1	TSL:6	n.*31G>A		downstream_gene	N/A

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

African (AFR) AF: 0.0469 AC: 3 AN: 64

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AF: 0.250 AC: 4 AN: 16

European-Finnish (FIN) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.224 AC: 234 AN: 1046

Other (OTH) AF: 0.286 AC: 12 AN: 42

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

African (AFR) AF: 0.193 AC: 7567 AN: 39158

American (AMR) AF: 0.399 AC: 5854 AN: 14668

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1585 AN: 3338

East Asian (EAS) AF: 0.711 AC: 3229 AN: 4542

South Asian (SAS) AF: 0.529 AC: 2417 AN: 4568

European-Finnish (FIN) AF: 0.524 AC: 5248 AN: 10018

Middle Eastern (MID) AF: 0.439 AC: 122 AN: 278

European-Non Finnish (NFE) AF: 0.465 AC: 30399 AN: 65334

Other (OTH) AF: 0.416 AC: 834 AN: 2006

Alfa AF: 0.207 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.064
DANN	Benign	0.54
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs157253; hg19: chr1-16840586;