rs763661174

Variant names:

• chr14-90644157-C-G
• rs763661174
• NM_001010854.2:c.1642G>C

Your query was ambiguous. Multiple possible variants found:

• chr14-90644157-C-G
• chr14-90644157-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001010854.2(TTC7B):​c.1642G>C​(p.Asp548His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: TTC7B NM_001010854.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.57

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]

TTC7B-AS1 (HGNC:56196): (TTC7B antisense RNA 1)

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TTC7B	NM_001010854.2	c.1642G>C	p.Asp548His	missense_variant	Exon 15 of 20	ENST00000328459.11	NP_001010854.1
TTC7B	NM_001401365.1	c.1642G>C	p.Asp548His	missense_variant	Exon 15 of 22		NP_001388294.1
TTC7B	NM_001320421.2	c.1336G>C	p.Asp446His	missense_variant	Exon 15 of 21		NP_001307350.1
TTC7B-AS1	NR_110134.1	n.103-587C>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TTC7B	ENST00000328459.11	c.1642G>C	p.Asp548His	missense_variant	Exon 15 of 20	1	NM_001010854.2	ENSP00000336127.4

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.69
BayesDel_addAF	Pathogenic	0.34	D
BayesDel_noAF	Pathogenic	0.25
CADD	Uncertain	25
DANN	Uncertain	0.99
DEOGEN2	Benign	0.27	T;T
Eigen	Pathogenic	0.75
Eigen_PC	Pathogenic	0.73
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.96	D;D
M_CAP	Benign	0.082	D
MetaRNN	Uncertain	0.69	D;D
MetaSVM	Uncertain	0.064	D
MutationAssessor	Benign	1.2	L;.
PrimateAI	Uncertain	0.77	T
PROVEAN	Benign	-0.79	N;N
REVEL	Uncertain	0.41
Sift	Benign	0.36	T;T
Sift4G	Benign	0.33	T;T
Polyphen		1.0	D;.
Vest4		0.84
MutPred		0.44		Gain of catalytic residue at Q545 (P = 0.0657);.;
MVP		0.58
MPC		1.2
ClinPred		0.93	D
GERP RS		5.8
Varity_R		0.33
gMVP		0.58

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: rs763661174; hg19: chr14-91110501;