14-90668317-C-A

Position:

• chr14-90668317-C-A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001010854.2(TTC7B):​c.1152+8206G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: TTC7B NM_001010854.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481

Genes affected

TTC7B (HGNC:19858): (tetratricopeptide repeat domain 7B) Involved in phosphatidylinositol phosphate biosynthetic process and protein localization to plasma membrane. Located in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TTC7B	NM_001010854.2	c.1152+8206G>T		intron_variant		ENST00000328459.11	NP_001010854.1
TTC7B	NM_001320421.2	c.846+8206G>T		intron_variant			NP_001307350.1
TTC7B	NM_001401365.1	c.1152+8206G>T		intron_variant			NP_001388294.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TTC7B	ENST00000328459.11	c.1152+8206G>T		intron_variant		1	NM_001010854.2	ENSP00000336127	P1
TTC7B	ENST00000554462.1	c.160+8206G>T		intron_variant		5		ENSP00000451928
TTC7B	ENST00000555005.5	c.375+8206G>T		intron_variant, NMD_transcript_variant		2		ENSP00000451825
TTC7B	ENST00000555239.5	c.194+8206G>T		intron_variant, NMD_transcript_variant		3		ENSP00000450520

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.3
DANN	Benign	0.76

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: rs961196; hg19: chr14-91134661;