rs7807677

Variant names:

• chr7-117862520-C-T
• rs7807677
• NM_033427.3:c.82-1204G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

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]

CTTNBP2 Gene-Disease associations (from GenCC):

• autism spectrum disorder

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CTTNBP2	NM_033427.3	c.82-1204G>A		intron_variant	Intron 1 of 22	ENST00000160373.8	NP_219499.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTTNBP2	ENST00000160373.8	c.82-1204G>A		intron_variant	Intron 1 of 22	1	NM_033427.3	ENSP00000160373.3

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

African (AFR) AF: 0.619 AC: 25638 AN: 41420

American (AMR) AF: 0.441 AC: 6733 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1599 AN: 3470

East Asian (EAS) AF: 0.412 AC: 2122 AN: 5146

South Asian (SAS) AF: 0.520 AC: 2502 AN: 4808

European-Finnish (FIN) AF: 0.645 AC: 6803 AN: 10548

Middle Eastern (MID) AF: 0.476 AC: 138 AN: 290

European-Non Finnish (NFE) AF: 0.565 AC: 38424 AN: 67962

Other (OTH) AF: 0.510 AC: 1080 AN: 2116

Alfa AF: 0.553 Hom.: 72764

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
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7807677; hg19: chr7-117502574;