rs2343

Positions:

• chr14-90628156-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.1752-10111G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 152,172 control chromosomes in the GnomAD database, including 11,362 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 0.38 (11362 hom., cov: 33)
• Consequence: TTC7B NM_001010854.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTC7B	NM_001010854.2	c.1752-10111G>A		intron_variant		ENST00000328459.11
TTC7B	NM_001320421.2	c.1446-10111G>A		intron_variant
TTC7B	NM_001401365.1	c.1752-10111G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC7B	ENST00000328459.11	c.1752-10111G>A		intron_variant		1	NM_001010854.2	P1

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58135 AN: 152054 Hom.: 11354 Cov.: 33

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.382 AC: 58176 AN: 152172 Hom.: 11362 Cov.: 33 AF XY: 0.384 AC XY: 28582 AN XY: 74400

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.349

Alfa AF: 0.396 Hom.: 6754

Bravo AF: 0.380

Asia WGS AF: 0.259 AC: 906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.46

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: rs2343; hg19: chr14-91094500;