Genetic Variant TTC28-AS1:n.145+2659G>C (chr22-27922204-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000419253.1(TTC28-AS1):n.145+2659G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0969 in 152,252 control chromosomes in the GnomAD database, including 801 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 0.097 ( 801 hom., cov: 32)

Failed GnomAD Quality Control

Consequence

TTC28-AS1
ENST00000419253.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.160

Publications

3 publications found

Variant links:

Genes affected

TTC28-AS1 (HGNC:29336): (TTC28 antisense RNA 1)

TTC28-AS1 links:

ENSG00000276150 (HGNC:):

ENSG00000276150 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TTC28-AS1	NR_026962.1 link	n.331+26G>C		intron_variant	Intron 2 of 2
TTC28-AS1	NR_026963.1 link	n.170+2659G>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TTC28-AS1	ENST00000419253.1 link	n.145+2659G>C	intron_variant	Intron 1 of 1	1
TTC28-AS1	ENST00000437713.8 link	n.319+26G>C	intron_variant	Intron 2 of 2	1
TTC28-AS1	ENST00000454741.5 link	n.125+2659G>C	intron_variant	Intron 1 of 4	1

Frequencies

GnomAD3 genomes

AF:

0.0968

AC:

14722

AN:

152134

Hom.:

796

Cov.:

show subpopulations

Gnomad AFR

AF:

0.135

Gnomad AMI

AF:

0.0581

Gnomad AMR

AF:

0.0809

Gnomad ASJ

AF:

0.0323

Gnomad EAS

AF:

0.00961

Gnomad SAS

AF:

0.0830

Gnomad FIN

AF:

0.109

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0874

Gnomad OTH

AF:

0.0793

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.0969

AC:

14747

AN:

152252

Hom.:

801

Cov.:

AF XY:

0.0963

AC XY:

7169

AN XY:

74442

show subpopulations

African (AFR)

AF:

0.135

AC:

5609

AN:

41546

American (AMR)

AF:

0.0814

AC:

1246

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0323

AC:

112

AN:

3472

East Asian (EAS)

AF:

0.00963

AC:

AN:

5190

South Asian (SAS)

AF:

0.0833

AC:

402

AN:

4828

European-Finnish (FIN)

AF:

0.109

AC:

1155

AN:

10602

Middle Eastern (MID)

AF:

0.0510

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0874

AC:

5940

AN:

67986

Other (OTH)

AF:

0.0780

AC:

165

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

674

1347

2021

2694

3368

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

172

344

516

688

860

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0455

Hom.:

Bravo

AF:

0.0970

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.46

(source)

DANN

Benign

0.37

PhyloP100

-0.16

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over