rs2105960

Variant names:

• chr6-30486012-A-C
• rs2105960
• ENST00000455094.1:n.73A>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

Genes affected

RANP1 (HGNC:21631): (RAN pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000455094.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RANP1	ENST00000455094.1	TSL:6	n.73A>C		non_coding_transcript_exon	Exon 1 of 1

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

African (AFR) AF: 0.356 AC: 9907 AN: 27846

American (AMR) AF: 0.340 AC: 15018 AN: 44188

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 10917 AN: 24288

East Asian (EAS) AF: 0.493 AC: 18856 AN: 38278

South Asian (SAS) AF: 0.450 AC: 36038 AN: 80024

European-Finnish (FIN) AF: 0.484 AC: 25625 AN: 52906

Middle Eastern (MID) AF: 0.360 AC: 1840 AN: 5110

European-Non Finnish (NFE) AF: 0.379 AC: 325758 AN: 860164

Other (OTH) AF: 0.384 AC: 19570 AN: 50932

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

African (AFR) AF: 0.358 AC: 14862 AN: 41470

American (AMR) AF: 0.361 AC: 5510 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1569 AN: 3470

East Asian (EAS) AF: 0.549 AC: 2837 AN: 5172

South Asian (SAS) AF: 0.449 AC: 2162 AN: 4818

European-Finnish (FIN) AF: 0.494 AC: 5217 AN: 10564

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.390 AC: 26490 AN: 67960

Other (OTH) AF: 0.363 AC: 765 AN: 2108

Alfa AF: 0.391 Hom.: 3600

Bravo AF: 0.381

Asia WGS AF: 0.440 AC: 1530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	4.8
DANN	Benign	0.61
PhyloP100		6.7

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2105960;

hg19: chr6-30453789;