rs2105960

Positions:

• chr6-30486012-A-C
• chr6-30486012-A-G

Variant summary

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

The ENST00000455094.1(RANP1):​n.73A>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.392 in 1,335,778 control chromosomes in the GnomAD database, including 105,704 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 0.39 (11910 hom., cov: 32)
  • Exomes 𝑓: 0.39 (93794 hom.)
• Consequence: RANP1 ENST00000455094.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.67

Genes affected

RANP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RANP1		n.30486012A>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RANP1	ENST00000455094.1	n.73A>C		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59830 AN: 151922 Hom.: 11902 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.360

GnomAD4 exome AF: 0.392 AC: 463529 AN: 1183736 Hom.: 93794 Cov.: 22 AF XY: 0.395 AC XY: 237625 AN XY: 600938

Gnomad4 AFR exome AF: 0.356

Gnomad4 AMR exome AF: 0.340

Gnomad4 ASJ exome AF: 0.449

Gnomad4 EAS exome AF: 0.493

Gnomad4 SAS exome AF: 0.450

Gnomad4 FIN exome AF: 0.484

Gnomad4 NFE exome AF: 0.379

Gnomad4 OTH exome AF: 0.384

GnomAD4 genome AF: 0.394 AC: 59869 AN: 152042 Hom.: 11910 Cov.: 32 AF XY: 0.400 AC XY: 29758 AN XY: 74332

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.549

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.363

Alfa AF: 0.389 Hom.: 1947

Bravo AF: 0.381

Asia WGS AF: 0.440 AC: 1530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	4.8
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2105960; hg19: chr6-30453789;