rs942740

chr14-90692525-G-Achr14-90692525-G-T

Variant summary

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

The NM_001010854.2(TTC7B):c.778-2813C>T 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 152,102 control chromosomes in the GnomAD database, including 2,108 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 (2108 hom., cov: 32)
• Consequence: TTC7B NM_001010854.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.371

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTC7B	NM_001010854.2	c.778-2813C>T		intron_variant		ENST00000328459.11
TTC7B	NM_001320421.2	c.472-2813C>T		intron_variant
TTC7B	NM_001401365.1	c.778-2813C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC7B	ENST00000328459.11	c.778-2813C>T		intron_variant		1	NM_001010854.2	P1
TTC7B	ENST00000557766.1	c.538-2813C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24821 AN: 151984 Hom.: 2108 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.0691

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.163 AC: 24832 AN: 152102 Hom.: 2108 Cov.: 32 AF XY: 0.162 AC XY: 12030 AN XY: 74350

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.0690

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.168

Alfa AF: 0.155 Hom.: 1198

Bravo AF: 0.159

Asia WGS AF: 0.103 AC: 359 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	2.7
Dann	Benign	0.73

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: rs942740; hg19: chr14-91158869;