rs1749715

chr14-90714816-G-A

Variant summary

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

The NM_001010854.2(TTC7B):c.698+15259C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.715 in 152,054 control chromosomes in the GnomAD database, including 39,860 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 0.72 (39860 hom., cov: 32)
• Consequence: TTC7B NM_001010854.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTC7B	NM_001010854.2	c.698+15259C>T		intron_variant		ENST00000328459.11
TTC7B	NM_001320421.2	c.392+15259C>T		intron_variant
TTC7B	NM_001401365.1	c.698+15259C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC7B	ENST00000328459.11	c.698+15259C>T		intron_variant		1	NM_001010854.2	P1
TTC7B	ENST00000557766.1	c.392+15259C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.715 AC: 108607 AN: 151936 Hom.: 39797 Cov.: 32

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.715 AC: 108736 AN: 152054 Hom.: 39860 Cov.: 32 AF XY: 0.713 AC XY: 53005 AN XY: 74320

Gnomad4 AFR AF: 0.878

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.512

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.635

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.691

Alfa AF: 0.686 Hom.: 5593

Bravo AF: 0.723

Asia WGS AF: 0.592 AC: 2056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.49
Dann	Benign	0.76

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: rs1749715; hg19: chr14-91181160;