chr14-90804831-C-G

Variant names:

• chr14-90804831-C-G
• rs1286318
• NM_001010854.2:c.121+11344G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001010854.2(TTC7B):​c.121+11344G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 152,136 control chromosomes in the GnomAD database, including 37,307 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 0.69 (37307 hom., cov: 33)
• Consequence: TTC7B NM_001010854.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.765 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC7B	NM_001010854.2	MANE Select	c.121+11344G>C		intron	N/A	NP_001010854.1	Q86TV6-1
	TTC7B	NM_001401365.1		c.121+11344G>C		intron	N/A	NP_001388294.1
	TTC7B	NM_001320421.2		c.-182+11344G>C		intron	N/A	NP_001307350.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC7B	ENST00000328459.11	TSL:1 MANE Select	c.121+11344G>C		intron	N/A	ENSP00000336127.4	Q86TV6-1
	TTC7B	ENST00000963264.1		c.121+11344G>C		intron	N/A	ENSP00000633323.1
	TTC7B	ENST00000963265.1		c.121+11344G>C		intron	N/A	ENSP00000633324.1

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104855 AN: 152018 Hom.: 37303 Cov.: 33

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.689 AC: 104891 AN: 152136 Hom.: 37307 Cov.: 33 AF XY: 0.691 AC XY: 51388 AN XY: 74390

African (AFR) AF: 0.500 AC: 20751 AN: 41462

American (AMR) AF: 0.767 AC: 11737 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.825 AC: 2864 AN: 3470

East Asian (EAS) AF: 0.694 AC: 3585 AN: 5162

South Asian (SAS) AF: 0.695 AC: 3353 AN: 4824

European-Finnish (FIN) AF: 0.747 AC: 7911 AN: 10594

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.770 AC: 52375 AN: 68008

Other (OTH) AF: 0.693 AC: 1464 AN: 2114

Alfa AF: 0.654 Hom.: 2286

Bravo AF: 0.688

Asia WGS AF: 0.646 AC: 2248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.61
PhyloP100		-1.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs1286318; hg19: chr14-91271175;