14-90804831-C-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TTC7B	NM_001010854.2	c.121+11344G>C		intron_variant	Intron 1 of 19	ENST00000328459.11	NP_001010854.1
TTC7B	NM_001401365.1	c.121+11344G>C		intron_variant	Intron 1 of 21		NP_001388294.1
TTC7B	NM_001320421.2	c.-182+11344G>C		intron_variant	Intron 1 of 20		NP_001307350.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TTC7B	ENST00000328459.11	c.121+11344G>C		intron_variant	Intron 1 of 19	1	NM_001010854.2	ENSP00000336127.4
TTC7B	ENST00000553948.1	c.-182+11344G>C		intron_variant	Intron 1 of 3	5		ENSP00000451201.1

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

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.767

Gnomad4 ASJ AF: 0.825

Gnomad4 EAS AF: 0.694

Gnomad4 SAS AF: 0.695

Gnomad4 FIN AF: 0.747

Gnomad4 NFE AF: 0.770

Gnomad4 OTH AF: 0.693

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.61
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs1286318; hg19: chr14-91271175;