10-88786215-T-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.945 AC: 8130 AN: 8600

American (AMR) AF: 0.865 AC: 21333 AN: 24656

Ashkenazi Jewish (ASJ) AF: 0.830 AC: 6106 AN: 7356

East Asian (EAS) AF: 0.999 AC: 13093 AN: 13112

South Asian (SAS) AF: 0.858 AC: 44020 AN: 51328

European-Finnish (FIN) AF: 0.739 AC: 12578 AN: 17018

Middle Eastern (MID) AF: 0.835 AC: 2143 AN: 2568

European-Non Finnish (NFE) AF: 0.694 AC: 104995 AN: 151376

Other (OTH) AF: 0.771 AC: 10949 AN: 14208

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

African (AFR) AF: 0.945 AC: 39252 AN: 41558

American (AMR) AF: 0.809 AC: 12361 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.825 AC: 2864 AN: 3472

East Asian (EAS) AF: 0.996 AC: 5160 AN: 5180

South Asian (SAS) AF: 0.865 AC: 4179 AN: 4830

European-Finnish (FIN) AF: 0.725 AC: 7665 AN: 10568

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.690 AC: 46903 AN: 67974

Other (OTH) AF: 0.802 AC: 1697 AN: 2116

Alfa AF: 0.734 Hom.: 131796

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
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs303478; hg19: chr10-90545972;