Variant chr6-13316852-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_016495.6(TBC1D7):c.382-144G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 962,006 control chromosomes in the GnomAD database, including 24,615 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.21 ( 3514 hom., cov: 32)

Exomes 𝑓: 0.21 ( 21101 hom. )

Consequence

TBC1D7
NM_016495.6 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.108

Variant links:

Genes affected

TBC1D7 (HGNC:21066): (TBC1 domain family member 7) This gene encodes a member of the TBC-domain containing protein family. The encoded protein functions as a subunit of the tuberous sclerosis TSC1-TSC2 complex which plays a role in the regulation of cellular growth and differentiation. Mutations in this gene have been associated with autosomal recessive megalencephaly. Alternative splicing results in multiple transcript variants. Naturally occurring readthrough transcription occurs between this locus and downstream LOC100130357. [provided by RefSeq, Jan 2016]

TBC1D7 links:

TBC1D7-LOC100130357 (HGNC:):

TBC1D7-LOC100130357 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BP6

Variant 6-13316852-C-A is Benign according to our data. Variant chr6-13316852-C-A is described in ClinVar as [Benign]. Clinvar id is 1228650.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TBC1D7	NM_016495.6 linkuse as main transcript	c.382-144G>T		intron_variant		ENST00000379300.8	NP_057579.1
TBC1D7-LOC100130357	NR_134872.2 linkuse as main transcript	n.472-144G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TBC1D7	ENST00000379300.8 linkuse as main transcript	c.382-144G>T		intron_variant		1	NM_016495.6	ENSP00000368602	P1	Q9P0N9-1

Frequencies

GnomAD3 genomes

AF:

0.206

AC:

31260

AN:

152046

Hom.:

3519

Cov.:

show subpopulations

Gnomad AFR

AF:

0.159

Gnomad AMI

AF:

0.170

Gnomad AMR

AF:

0.245

Gnomad ASJ

AF:

0.235

Gnomad EAS

AF:

0.415

Gnomad SAS

AF:

0.386

Gnomad FIN

AF:

0.157

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.203

Gnomad OTH

AF:

0.207

GnomAD4 exome

AF:

0.213

AC:

172371

AN:

809840

Hom.:

21101

AF XY:

0.219

AC XY:

91062

AN XY:

415870

show subpopulations

Gnomad4 AFR exome

AF:

0.158

Gnomad4 AMR exome

AF:

0.261

Gnomad4 ASJ exome

AF:

0.237

Gnomad4 EAS exome

AF:

0.392

Gnomad4 SAS exome

AF:

0.365

Gnomad4 FIN exome

AF:

0.151

Gnomad4 NFE exome

AF:

0.190

Gnomad4 OTH exome

AF:

0.216

GnomAD4 genome

AF:

0.205

AC:

31263

AN:

152166

Hom.:

3514

Cov.:

AF XY:

0.208

AC XY:

15505

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.159

Gnomad4 AMR

AF:

0.245

Gnomad4 ASJ

AF:

0.235

Gnomad4 EAS

AF:

0.415

Gnomad4 SAS

AF:

0.383

Gnomad4 FIN

AF:

0.157

Gnomad4 NFE

AF:

0.203

Gnomad4 OTH

AF:

0.211

Alfa

AF:

0.209

Hom.:

4590

Bravo

AF:

0.205

Asia WGS

AF:

0.387

AC:

1344

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 21, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.1

DANN

Benign

0.68

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