rs7807677

chr7-117862520-C-T

Variant summary

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

The NM_033427.3(CTTNBP2):c.82-1204G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 151,932 control chromosomes in the GnomAD database, including 24,460 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 0.56 (24460 hom., cov: 31)
• Consequence: CTTNBP2 NM_033427.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82

Genes affected

CTTNBP2 (HGNC:15679): (cortactin binding protein 2) This gene encodes a protein with six ankyrin repeats and several proline-rich regions. A similar gene in rat interacts with a central regulator of the actin cytoskeleton. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTTNBP2	NM_033427.3	c.82-1204G>A		intron_variant		ENST00000160373.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTTNBP2	ENST00000160373.8	c.82-1204G>A		intron_variant		1	NM_033427.3	P1

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85279 AN: 151810 Hom.: 24431 Cov.: 31

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.562 AC: 85355 AN: 151932 Hom.: 24460 Cov.: 31 AF XY: 0.565 AC XY: 41913 AN XY: 74234

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.461

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.510

Alfa AF: 0.549 Hom.: 46689

Bravo AF: 0.544

Asia WGS AF: 0.457 AC: 1589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	0.61
Dann	Benign	0.78

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7807677; hg19: chr7-117502574;