14-90723633-G-T

Variant names:

• chr14-90723633-G-T
• rs8018904
• NM_001010854.2:c.698+6442C>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.698+6442C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,110 control chromosomes in the GnomAD database, including 2,355 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 0.14 (2355 hom., cov: 32)
• Consequence: TTC7B NM_001010854.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500
• Publications: 2 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TTC7B	NM_001010854.2	c.698+6442C>A		intron_variant	Intron 5 of 19	ENST00000328459.11	NP_001010854.1
TTC7B	NM_001401365.1	c.698+6442C>A		intron_variant	Intron 5 of 21		NP_001388294.1
TTC7B	NM_001320421.2	c.392+6442C>A		intron_variant	Intron 5 of 20		NP_001307350.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TTC7B	ENST00000328459.11	c.698+6442C>A		intron_variant	Intron 5 of 19	1	NM_001010854.2	ENSP00000336127.4
TTC7B	ENST00000557766.1	c.392+6442C>A		intron_variant	Intron 4 of 6	3		ENSP00000451238.1

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21247 AN: 151992 Hom.: 2356 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.0843

Gnomad ASJ AF: 0.0706

Gnomad EAS AF: 0.0554

Gnomad SAS AF: 0.0580

Gnomad FIN AF: 0.0767

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0740

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.140 AC: 21264 AN: 152110 Hom.: 2355 Cov.: 32 AF XY: 0.136 AC XY: 10135 AN XY: 74358

African (AFR) AF: 0.315 AC: 13045 AN: 41440

American (AMR) AF: 0.0842 AC: 1287 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0706 AC: 245 AN: 3472

East Asian (EAS) AF: 0.0553 AC: 286 AN: 5168

South Asian (SAS) AF: 0.0583 AC: 281 AN: 4824

European-Finnish (FIN) AF: 0.0767 AC: 813 AN: 10594

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0741 AC: 5036 AN: 68008

Other (OTH) AF: 0.102 AC: 214 AN: 2108

Alfa AF: 0.0924 Hom.: 3044

Bravo AF: 0.149

Asia WGS AF: 0.0830 AC: 287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.84
PhyloP100		-0.050
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: rs8018904; hg19: chr14-91189977;