rs7089349

Positions:

• chr10-94647595-T-C

Variant summary

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

The ENST00000434549.1(CTBP2P2):​n.402A>G 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 0.167 in 179,966 control chromosomes in the GnomAD database, including 2,773 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 0.17 (2356 hom., cov: 31)
  • Exomes 𝑓: 0.16 (417 hom.)
• Consequence: CTBP2P2 ENST00000434549.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.199

Genes affected

CTBP2P2 (HGNC:45194): (CTBP2 pseudogene 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CTBP2P2	ENST00000434549.1	n.402A>G		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25559 AN: 152064 Hom.: 2351 Cov.: 31

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.149

GnomAD4 exome AF: 0.158 AC: 4396 AN: 27784 Hom.: 417 Cov.: 0 AF XY: 0.171 AC XY: 2475 AN XY: 14482

Gnomad4 AFR exome AF: 0.134

Gnomad4 AMR exome AF: 0.109

Gnomad4 ASJ exome AF: 0.118

Gnomad4 EAS exome AF: 0.268

Gnomad4 SAS exome AF: 0.308

Gnomad4 FIN exome AF: 0.150

Gnomad4 NFE exome AF: 0.131

Gnomad4 OTH exome AF: 0.151

GnomAD4 genome AF: 0.168 AC: 25579 AN: 152182 Hom.: 2356 Cov.: 31 AF XY: 0.172 AC XY: 12831 AN XY: 74394

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.154

Alfa AF: 0.146 Hom.: 326

Bravo AF: 0.161

Asia WGS AF: 0.305 AC: 1057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	0.019
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7089349; hg19: chr10-96407352;