rs1891321

Positions:

• chr1-19970922-G-A

Variant summary

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

The 1-19970922-G-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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RN7SL304P	ENST00000488028.3			upstream_gene_variant

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;