10-45147086-G-A

Position:

• chr10-45147086-G-A

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400

Genes affected

(HGNC:):

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

ACMG classification

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	n.263-141C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000448600.5	n.90-141C>T		intron_variant, non_coding_transcript_variant		1
CUBNP3	ENST00000457461.1	n.1397-381G>A		intron_variant, non_coding_transcript_variant
	ENST00000619977.1	n.263-141C>T		intron_variant, non_coding_transcript_variant		1
	ENST00000661630.1	n.146-4932C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.955 AC: 145329 AN: 152238 Hom.: 69435 Cov.: 34

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.: 0 AF XY: 0.958 AC XY: 4838 AN XY: 5048

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.: 34 AF XY: 0.955 AC XY: 71124 AN XY: 74490

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

Other links and lift over

dbSNP: rs1339746; hg19: chr10-45642534;