rs1998591

Variant names:

• chr10-94648221-G-A
• rs1998591
• ENST00000434549.1:n.-225C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000434549.1(CTBP2P2):​n.-225C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,114 control chromosomes in the GnomAD database, including 6,445 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 0.28 (6445 hom., cov: 33)
• Consequence: CTBP2P2 ENST00000434549.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 8 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=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.44 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.-225C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42209 AN: 151996 Hom.: 6434 Cov.: 33

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.250

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.278 AC: 42251 AN: 152114 Hom.: 6445 Cov.: 33 AF XY: 0.281 AC XY: 20912 AN XY: 74364

African (AFR) AF: 0.389 AC: 16139 AN: 41466

American (AMR) AF: 0.201 AC: 3080 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 741 AN: 3464

East Asian (EAS) AF: 0.412 AC: 2129 AN: 5162

South Asian (SAS) AF: 0.455 AC: 2195 AN: 4820

European-Finnish (FIN) AF: 0.234 AC: 2479 AN: 10592

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14702 AN: 67998

Other (OTH) AF: 0.256 AC: 541 AN: 2112

Alfa AF: 0.232 Hom.: 12126

Bravo AF: 0.274

Asia WGS AF: 0.443 AC: 1538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.23
PhyloP100		-1.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1998591;

hg19: chr10-96407978;