10-88786215-T-G

Variant names:

• chr10-88786215-T-G
• rs303478
• ENST00000453021.1:n.847A>C

Variant summary

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

The ENST00000453021.1(RCBTB2P1):​n.847A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.779 in 442,410 control chromosomes in the GnomAD database, including 136,683 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 0.80 (49239 hom., cov: 32)
  • Exomes 𝑓: 0.77 (87444 hom.)
• Consequence: RCBTB2P1 ENST00000453021.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.458

Genes affected

RCBTB2P1 (HGNC:45167): (RCC1 and BTB domain containing protein 2 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RCBTB2P1		n.88786215T>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RCBTB2P1	ENST00000453021.1	n.847A>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.796 AC: 121012 AN: 152068 Hom.: 49169 Cov.: 32

Gnomad AFR AF: 0.944

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.800

GnomAD4 exome AF: 0.770 AC: 223347 AN: 290222 Hom.: 87444 Cov.: 0 AF XY: 0.776 AC XY: 124275 AN XY: 160226

Gnomad4 AFR exome AF: 0.945

Gnomad4 AMR exome AF: 0.865

Gnomad4 ASJ exome AF: 0.830

Gnomad4 EAS exome AF: 0.999

Gnomad4 SAS exome AF: 0.858

Gnomad4 FIN exome AF: 0.739

Gnomad4 NFE exome AF: 0.694

Gnomad4 OTH exome AF: 0.771

GnomAD4 genome AF: 0.796 AC: 121142 AN: 152188 Hom.: 49239 Cov.: 32 AF XY: 0.800 AC XY: 59512 AN XY: 74400

Gnomad4 AFR AF: 0.945

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.825

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.865

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.690

Gnomad4 OTH AF: 0.802

Alfa AF: 0.720 Hom.: 82777

Bravo AF: 0.809

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs303478; hg19: chr10-90545972;