14-90692525-G-A

Variant names:

• chr14-90692525-G-A
• rs942740
• NM_001010854.2:c.778-2813C>T

Variant summary

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

The NM_001010854.2(TTC7B):​c.778-2813C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,102 control chromosomes in the GnomAD database, including 2,108 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 0.16 (2108 hom., cov: 32)
• Consequence: TTC7B NM_001010854.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.371
• Publications: 5 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.174 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC7B	NM_001010854.2	MANE Select	c.778-2813C>T		intron	N/A	NP_001010854.1
	TTC7B	NM_001401365.1		c.778-2813C>T		intron	N/A	NP_001388294.1
	TTC7B	NM_001320421.2		c.472-2813C>T		intron	N/A	NP_001307350.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC7B	ENST00000328459.11	TSL:1 MANE Select	c.778-2813C>T		intron	N/A	ENSP00000336127.4
	TTC7B	ENST00000557766.1	TSL:3	c.538-2813C>T		intron	N/A	ENSP00000451238.1

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24821 AN: 151984 Hom.: 2108 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.0691

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.163 AC: 24832 AN: 152102 Hom.: 2108 Cov.: 32 AF XY: 0.162 AC XY: 12030 AN XY: 74350

African (AFR) AF: 0.157 AC: 6515 AN: 41480

American (AMR) AF: 0.124 AC: 1896 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 722 AN: 3470

East Asian (EAS) AF: 0.0690 AC: 358 AN: 5186

South Asian (SAS) AF: 0.138 AC: 666 AN: 4830

European-Finnish (FIN) AF: 0.189 AC: 1992 AN: 10566

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11989 AN: 67974

Other (OTH) AF: 0.168 AC: 354 AN: 2112

Alfa AF: 0.157 Hom.: 1332

Bravo AF: 0.159

Asia WGS AF: 0.103 AC: 359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.7
DANN	Benign	0.73
PhyloP100		0.37
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: rs942740; hg19: chr14-91158869;