7-117721135-TAAAAA-TAAA

Variant names:

• chr7-117721135-TAA-T
• rs764589410
• NM_033427.3:c.4448-7_4448-6delTT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_033427.3(CTTNBP2):​c.4448-7_4448-6delTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: CTTNBP2 NM_033427.3 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.09

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]

LOC105375469 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CTTNBP2	NM_033427.3	c.4448-7_4448-6delTT		splice_region_variant, intron_variant	Intron 19 of 22	ENST00000160373.8	NP_219499.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTTNBP2	ENST00000160373.8	c.4448-7_4448-6delTT		splice_region_variant, intron_variant	Intron 19 of 22	1	NM_033427.3	ENSP00000160373.3
CTTNBP2	ENST00000446636.5	c.2909-7_2909-6delTT		splice_region_variant, intron_variant	Intron 17 of 20	5		ENSP00000389576.1
CTTNBP2	ENST00000441556.5	n.*2362-7_*2362-6delTT		splice_region_variant, intron_variant	Intron 19 of 22	5		ENSP00000397678.1
CTTNBP2	ENST00000445366.1	n.*165-7_*165-6delTT		splice_region_variant, intron_variant	Intron 2 of 5	5		ENSP00000389491.1

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs764589410; hg19: chr7-117361189;