Variant 14-37749343-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001310135.5(TTC6):c.2768G>A(p.Arg923His) variant causes a missense change. The variant allele was found at a frequency of 0.00609 in 1,491,782 control chromosomes in the GnomAD database, including 116 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0071 ( 15 hom., cov: 33)

Exomes 𝑓: 0.0060 ( 101 hom. )

Consequence

TTC6
NM_001310135.5 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.80

Variant links:

Genes affected

TTC6 (HGNC:19739): (tetratricopeptide repeat domain 6)

TTC6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.011599302).

BP6

Variant 14-37749343-G-A is Benign according to our data. Variant chr14-37749343-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2644185.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 15 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TTC6	NM_001310135.5 linkuse as main transcript	c.2768G>A	p.Arg923His	missense_variant	13/33	ENST00000553443.6	NP_001297064.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TTC6	ENST00000553443.6 linkuse as main transcript	c.2768G>A	p.Arg923His	missense_variant	13/33	5	NM_001310135.5	ENSP00000451131	P1
TTC6	ENST00000533625.5 linkuse as main transcript	c.*1062+10188G>A		intron_variant, NMD_transcript_variant		2		ENSP00000451566

Frequencies

GnomAD3 genomes

AF:

0.00714

AC:

1086

AN:

152142

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000507

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00255

Gnomad ASJ

AF:

0.00548

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.0264

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0104

Gnomad OTH

AF:

0.00814

GnomAD3 exomes

AF:

0.00548

AC:

590

AN:

107608

Hom.:

AF XY:

0.00511

AC XY:

299

AN XY:

58560

show subpopulations

Gnomad AFR exome

AF:

0.000333

Gnomad AMR exome

AF:

0.00232

Gnomad ASJ exome

AF:

0.00728

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000187

Gnomad FIN exome

AF:

0.0309

Gnomad NFE exome

AF:

0.00777

Gnomad OTH exome

AF:

0.00533

GnomAD4 exome

AF:

0.00597

AC:

8001

AN:

1339522

Hom.:

101

Cov.:

AF XY:

0.00604

AC XY:

3957

AN XY:

655552

show subpopulations

Gnomad4 AFR exome

AF:

0.000469

Gnomad4 AMR exome

AF:

0.00200

Gnomad4 ASJ exome

AF:

0.00685

Gnomad4 EAS exome

AF:

0.0000285

Gnomad4 SAS exome

AF:

0.000113

Gnomad4 FIN exome

AF:

0.0274

Gnomad4 NFE exome

AF:

0.00622

Gnomad4 OTH exome

AF:

0.00480

GnomAD4 genome

AF:

0.00713

AC:

1086

AN:

152260

Hom.:

Cov.:

AF XY:

0.00760

AC XY:

566

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.000505

Gnomad4 AMR

AF:

0.00255

Gnomad4 ASJ

AF:

0.00548

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000414

Gnomad4 FIN

AF:

0.0264

Gnomad4 NFE

AF:

0.0104

Gnomad4 OTH

AF:

0.00806

Alfa

AF:

0.0114

Hom.:

Bravo

AF:

0.00408

TwinsUK

AF:

0.00189

AC:

ALSPAC

AF:

0.00363

AC:

ExAC

AF:

0.00211

AC:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Sep 01, 2023

TTC6: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.34

BayesDel_noAF

Benign

-0.25

CADD

Pathogenic

DANN

Pathogenic

1.0

DEOGEN2

Uncertain

0.75

Eigen

Uncertain

0.42

Eigen_PC

Uncertain

0.52

FATHMM_MKL

Uncertain

0.96

LIST_S2

Benign

0.67

MetaRNN

Benign

0.012

MetaSVM

Benign

-0.33

PROVEAN

Uncertain

-3.6

REVEL

Uncertain

0.44

Sift

Uncertain

0.0030

Sift4G

Pathogenic

0.0

Vest4

0.49

MVP

0.82

MPC

0.26

ClinPred

0.051

GERP RS

5.8

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over