rs7089349

Variant names:

• chr10-94647595-T-C
• rs7089349
• ENST00000434549.1:n.402A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000434549.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTBP2P2	ENST00000434549.1	TSL:6	n.402A>G		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.134 AC: 113 AN: 846

American (AMR) AF: 0.109 AC: 168 AN: 1542

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 94 AN: 794

East Asian (EAS) AF: 0.268 AC: 235 AN: 876

South Asian (SAS) AF: 0.308 AC: 1087 AN: 3534

European-Finnish (FIN) AF: 0.150 AC: 177 AN: 1180

Middle Eastern (MID) AF: 0.113 AC: 14 AN: 124

European-Non Finnish (NFE) AF: 0.131 AC: 2249 AN: 17174

Other (OTH) AF: 0.151 AC: 259 AN: 1714

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

African (AFR) AF: 0.176 AC: 7315 AN: 41526

American (AMR) AF: 0.132 AC: 2017 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 456 AN: 3470

East Asian (EAS) AF: 0.312 AC: 1607 AN: 5156

South Asian (SAS) AF: 0.333 AC: 1610 AN: 4828

European-Finnish (FIN) AF: 0.183 AC: 1935 AN: 10592

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10123 AN: 67996

Other (OTH) AF: 0.154 AC: 326 AN: 2116

Alfa AF: 0.146 Hom.: 387

Bravo AF: 0.161

Asia WGS AF: 0.305 AC: 1057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	0.019
DANN	Benign	0.28
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs7089349; hg19: chr10-96407352;