rs7656416

chr4-1260747-C-T

Variant summary

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

The ENST00000578730.2(CTBP1-DT):n.2602+8925C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0987 in 151,802 control chromosomes in the GnomAD database, including 1,170 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 0.099 (1170 hom., cov: 32)
• Consequence: CTBP1-DT ENST00000578730.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.24

Genes affected

CTBP1-DT (HGNC:28307): (CTBP1 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.15).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTBP1-DT	ENST00000578730.2	n.2602+8925C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0983 AC: 14917 AN: 151690 Hom.: 1156 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.0845

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0720

Gnomad MID AF: 0.0414

Gnomad NFE AF: 0.0398

Gnomad OTH AF: 0.0761

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

GnomAD4 genome AF: 0.0987 AC: 14983 AN: 151802 Hom.: 1170 Cov.: 32 AF XY: 0.104 AC XY: 7690 AN XY: 74192

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.0845

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.0720

Gnomad4 NFE AF: 0.0398

Gnomad4 OTH AF: 0.0768

Alfa AF: 0.0546 Hom.: 141

Bravo AF: 0.114

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.81
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7656416; hg19: chr4-1254535;