chr14-90628156-C-T

Variant names:

• chr14-90628156-C-T
• rs2343
• NM_001010854.2:c.1752-10111G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001010854.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC7B	NM_001010854.2	MANE Select	c.1752-10111G>A		intron	N/A	NP_001010854.1
	TTC7B	NM_001401365.1		c.1752-10111G>A		intron	N/A	NP_001388294.1
	TTC7B	NM_001320421.2		c.1446-10111G>A		intron	N/A	NP_001307350.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC7B	ENST00000328459.11	TSL:1 MANE Select	c.1752-10111G>A		intron	N/A	ENSP00000336127.4
	TTC7B	ENST00000553972.5	TSL:1	c.162-10111G>A		intron	N/A	ENSP00000451440.1
	TTC7B	ENST00000554654.5	TSL:3	n.290-10111G>A		intron	N/A

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

African (AFR) AF: 0.342 AC: 14201 AN: 41506

American (AMR) AF: 0.438 AC: 6701 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1247 AN: 3468

East Asian (EAS) AF: 0.226 AC: 1173 AN: 5188

South Asian (SAS) AF: 0.331 AC: 1597 AN: 4824

European-Finnish (FIN) AF: 0.431 AC: 4558 AN: 10582

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27366 AN: 67992

Other (OTH) AF: 0.349 AC: 739 AN: 2116

Alfa AF: 0.388 Hom.: 9905

Bravo AF: 0.380

Asia WGS AF: 0.259 AC: 906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.46
PhyloP100		-0.23
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: rs2343; hg19: chr14-91094500;