rs17793829

Positions:

• chr14-90555841-C-T

Variant summary

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

The NM_001010854.2(TTC7B):​c.2311-14252G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,286 control chromosomes in the GnomAD database, including 2,476 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 0.16 (2476 hom., cov: 33)
• Consequence: TTC7B NM_001010854.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.413

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]

TTC7B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TTC7B	NM_001010854.2	c.2311-14252G>A		intron_variant		ENST00000328459.11	NP_001010854.1
TTC7B	NM_001401365.1	c.2524-14252G>A		intron_variant			NP_001388294.1
TTC7B	NM_001320421.2	c.2056-14252G>A		intron_variant			NP_001307350.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TTC7B	ENST00000328459.11	c.2311-14252G>A		intron_variant		1	NM_001010854.2	ENSP00000336127.4

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24807 AN: 152168 Hom.: 2470 Cov.: 33

Gnomad AFR AF: 0.0550

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.163 AC: 24822 AN: 152286 Hom.: 2476 Cov.: 33 AF XY: 0.168 AC XY: 12530 AN XY: 74462

Gnomad4 AFR AF: 0.0548

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.171

Alfa AF: 0.197 Hom.: 6127

Bravo AF: 0.148

Asia WGS AF: 0.182 AC: 633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.3
DANN	Benign	0.81

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: rs17793829; hg19: chr14-91022185;