Genetic Variant ENST00000419253.1: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:

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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

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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