rs1891321

Variant names:

• chr1-19970922-G-A
• rs1891321
• ENST00000488028.3:n.-47G>A

Variant summary

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

The ENST00000488028.3(RN7SL304P):​n.-47G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 151,998 control chromosomes in the GnomAD database, including 12,988 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 0.41 (12987 hom., cov: 32)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: RN7SL304P ENST00000488028.3 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.322

Genes affected

RN7SL304P (HGNC:46320): (RNA, 7SL, cytoplasmic 304, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.432 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
RN7SL304P	ENST00000488028.3	n.-47G>A		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62286 AN: 151876 Hom.: 12971 Cov.: 32

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.292

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.393

GnomAD4 exome AF: 0.500 AC: 2 AN: 4 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.410 AC: 62356 AN: 151994 Hom.: 12987 Cov.: 32 AF XY: 0.410 AC XY: 30500 AN XY: 74300

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.395

Alfa AF: 0.403 Hom.: 1735

Bravo AF: 0.405

Asia WGS AF: 0.302 AC: 1053 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.3
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1891321; hg19: chr1-20297415;