rs7656416

Variant names:

• chr4-1260747-C-T
• rs7656416
• ENST00000505364.1:n.1600-4593C>T

Variant summary

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

The ENST00000505364.1(CTBP1-DT):​n.1600-4593C>T variant causes a intron 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 ENST00000505364.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.24
• Publications: 34 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505364.1. 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
	CTBP1-DT	ENST00000505364.1	TSL:2	n.1600-4593C>T		intron	N/A
	CTBP1-DT	ENST00000578730.2	TSL:2	n.2602+8925C>T		intron	N/A
	CTBP1-DT	ENST00000670838.1		n.2064-4593C>T		intron	N/A

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

African (AFR) AF: 0.132 AC: 5470 AN: 41334

American (AMR) AF: 0.211 AC: 3215 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0845 AC: 293 AN: 3466

East Asian (EAS) AF: 0.323 AC: 1657 AN: 5136

South Asian (SAS) AF: 0.146 AC: 696 AN: 4760

European-Finnish (FIN) AF: 0.0720 AC: 762 AN: 10586

Middle Eastern (MID) AF: 0.0445 AC: 13 AN: 292

European-Non Finnish (NFE) AF: 0.0398 AC: 2707 AN: 67962

Other (OTH) AF: 0.0768 AC: 162 AN: 2110

Alfa AF: 0.0709 Hom.: 886

Bravo AF: 0.114

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.81
DANN	Benign	0.79
PhyloP100		-4.2

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: rs7656416;

hg19: chr4-1254535;