rs17793829

Variant names:

• chr14-90555841-C-T
• rs17793829
• NM_001010854.2:c.2311-14252G>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.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
• Publications: 9 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=-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 rank	MANE	Protein	UniProt
TTC7B	NM_001010854.2	c.2311-14252G>A		intron_variant	Intron 19 of 19	ENST00000328459.11	NP_001010854.1
TTC7B	NM_001401365.1	c.2524-14252G>A		intron_variant	Intron 21 of 21		NP_001388294.1
TTC7B	NM_001320421.2	c.2056-14252G>A		intron_variant	Intron 20 of 20		NP_001307350.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TTC7B	ENST00000328459.11	c.2311-14252G>A		intron_variant	Intron 19 of 19	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

African (AFR) AF: 0.0548 AC: 2281 AN: 41590

American (AMR) AF: 0.177 AC: 2703 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 725 AN: 3472

East Asian (EAS) AF: 0.113 AC: 585 AN: 5174

South Asian (SAS) AF: 0.234 AC: 1132 AN: 4830

European-Finnish (FIN) AF: 0.277 AC: 2941 AN: 10606

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13965 AN: 67994

Other (OTH) AF: 0.171 AC: 362 AN: 2116

Alfa AF: 0.188 Hom.: 8841

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
PhyloP100		-0.41
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: rs17793829; hg19: chr14-91022185;