Genetic Variant TIGD6:p.Glu345LysfsTer11 (chr5-149995316-CT-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_030953.4(TIGD6):c.1032delA(p.Glu345LysfsTer11) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.57 ( 25394 hom., cov: 0)

Exomes 𝑓: 0.64 ( 299692 hom. )

Consequence

TIGD6
NM_030953.4 frameshift

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0910

Variant links:

Genes affected

TIGD6 (HGNC:18332): (tigger transposable element derived 6) The protein encoded by this gene belongs to the tigger subfamily of the pogo superfamily of DNA-mediated transposons in humans. These proteins are related to DNA transposons found in fungi and nematodes, and more distantly to the Tc1 and mariner transposases. They are also very similar to the major mammalian centromere protein B. [provided by RefSeq, Oct 2009]

TIGD6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 5-149995316-CT-C is Benign according to our data. Variant chr5-149995316-CT-C is described in ClinVar as [Benign]. Clinvar id is 1273227.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TIGD6	NM_030953.4 link	c.1032delA	p.Glu345LysfsTer11	frameshift_variant	Exon 2 of 2	ENST00000296736.4	NP_112215.1	Q17RP2
TIGD6	NM_001243253.2 link	c.1032delA	p.Glu345LysfsTer11	frameshift_variant	Exon 2 of 2		NP_001230182.1	Q17RP2
TIGD6	NM_001412172.1 link	c.1032delA	p.Glu345LysfsTer11	frameshift_variant	Exon 3 of 3		NP_001399101.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TIGD6	ENST00000296736.4 link	c.1032delA	p.Glu345LysfsTer11	frameshift_variant	Exon 2 of 2	1	NM_030953.4	ENSP00000296736.3		Q17RP2
TIGD6	ENST00000515406.2 link	c.1032delA	p.Glu345LysfsTer11	frameshift_variant	Exon 2 of 2	1		ENSP00000425318.2		Q17RP2

Frequencies

GnomAD3 genomes

AF:

0.567

AC:

86082

AN:

151896

Hom.:

25376

Cov.:

show subpopulations

Gnomad AFR

AF:

0.411

Gnomad AMI

AF:

0.645

Gnomad AMR

AF:

0.473

Gnomad ASJ

AF:

0.619

Gnomad EAS

AF:

0.596

Gnomad SAS

AF:

0.591

Gnomad FIN

AF:

0.681

Gnomad MID

AF:

0.487

Gnomad NFE

AF:

0.658

Gnomad OTH

AF:

0.556

GnomAD3 exomes

AF:

0.596

AC:

149923

AN:

251454

Hom.:

46030

AF XY:

0.604

AC XY:

82088

AN XY:

135896

show subpopulations

Gnomad AFR exome

AF:

0.407

Gnomad AMR exome

AF:

0.432

Gnomad ASJ exome

AF:

0.608

Gnomad EAS exome

AF:

0.623

Gnomad SAS exome

AF:

0.584

Gnomad FIN exome

AF:

0.675

Gnomad NFE exome

AF:

0.656

Gnomad OTH exome

AF:

0.606

GnomAD4 exome

AF:

0.637

AC:

931170

AN:

1461884

Hom.:

299692

Cov.:

AF XY:

0.637

AC XY:

463285

AN XY:

727242

show subpopulations

Gnomad4 AFR exome

AF:

0.407

Gnomad4 AMR exome

AF:

0.436

Gnomad4 ASJ exome

AF:

0.618

Gnomad4 EAS exome

AF:

0.560

Gnomad4 SAS exome

AF:

0.586

Gnomad4 FIN exome

AF:

0.678

Gnomad4 NFE exome

AF:

0.659

Gnomad4 OTH exome

AF:

0.618

GnomAD4 genome

AF:

0.567

AC:

86141

AN:

152014

Hom.:

25394

Cov.:

AF XY:

0.566

AC XY:

42063

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.411

Gnomad4 AMR

AF:

0.473

Gnomad4 ASJ

AF:

0.619

Gnomad4 EAS

AF:

0.596

Gnomad4 SAS

AF:

0.592

Gnomad4 FIN

AF:

0.681

Gnomad4 NFE

AF:

0.658

Gnomad4 OTH

AF:

0.553

Alfa

AF:

0.618

Hom.:

5304

Bravo

AF:

0.543

Asia WGS

AF:

0.567

AC:

1972

AN:

3478

EpiCase

AF:

0.640

EpiControl

AF:

0.634

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Oct 17, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 27421018) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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