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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTBP1-DT	ENST00000505364.1	n.1600-4593C>T		intron_variant	Intron 1 of 1	2
CTBP1-DT	ENST00000578730.2	n.2602+8925C>T		intron_variant	Intron 1 of 2	2
CTBP1-DT	ENST00000670838.1	n.2064-4593C>T		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs7656416; hg19: chr4-1254535;