Variant rs1339746 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_024472.1(RSU1P2):n.263-141C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.955 in 162,038 control chromosomes in the GnomAD database, including 73,974 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 0.95 ( 69497 hom., cov: 34)

Exomes 𝑓: 0.96 ( 4477 hom. )

Consequence

RSU1P2
NR_024472.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0400

Variant links:

Genes affected

(HGNC:):

links:

CUBNP3 (HGNC:44985): (cubilin pseudogene 3)

CUBNP3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.98 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RSU1P2	NR_024472.1 linkuse as main transcript	n.263-141C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
	ENST00000448600.5 linkuse as main transcript	n.90-141C>T	intron_variant, non_coding_transcript_variant	1
CUBNP3	ENST00000457461.1 linkuse as main transcript	n.1397-381G>A	intron_variant, non_coding_transcript_variant
	ENST00000619977.1 linkuse as main transcript	n.263-141C>T	intron_variant, non_coding_transcript_variant	1
	ENST00000661630.1 linkuse as main transcript	n.146-4932C>T	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.955

AC:

145329

AN:

152238

Hom.:

69435

Cov.:

show subpopulations

Gnomad AFR

AF:

0.988

Gnomad AMI

AF:

0.846

Gnomad AMR

AF:

0.959

Gnomad ASJ

AF:

0.941

Gnomad EAS

AF:

0.999

Gnomad SAS

AF:

0.983

Gnomad FIN

AF:

0.923

Gnomad MID

AF:

0.959

Gnomad NFE

AF:

0.935

Gnomad OTH

AF:

0.951

GnomAD4 exome

AF:

0.961

AC:

9306

AN:

9682

Hom.:

4477

Cov.:

AF XY:

0.958

AC XY:

4838

AN XY:

5048

show subpopulations

Gnomad4 AFR exome

AF:

0.987

Gnomad4 AMR exome

AF:

0.977

Gnomad4 ASJ exome

AF:

0.965

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.991

Gnomad4 FIN exome

AF:

0.896

Gnomad4 NFE exome

AF:

0.950

Gnomad4 OTH exome

AF:

0.945

GnomAD4 genome

AF:

0.955

AC:

145450

AN:

152356

Hom.:

69497

Cov.:

AF XY:

0.955

AC XY:

71124

AN XY:

74490

show subpopulations

Gnomad4 AFR

AF:

0.988

Gnomad4 AMR

AF:

0.959

Gnomad4 ASJ

AF:

0.941

Gnomad4 EAS

AF:

0.999

Gnomad4 SAS

AF:

0.983

Gnomad4 FIN

AF:

0.923

Gnomad4 NFE

AF:

0.935

Gnomad4 OTH

AF:

0.952

Alfa

AF:

0.942

Hom.:

13697

Bravo

AF:

0.960

Asia WGS

AF:

0.988

AC:

3434

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.58

DANN

Benign

0.86

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over