Genetic Variant KTN1-AS1:n.388-18801C>T (chr14-55518294-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000554558.6(KTN1-AS1):n.388-18801C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 152,092 control chromosomes in the GnomAD database, including 26,080 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 0.58 ( 26080 hom., cov: 32)

Consequence

KTN1-AS1
ENST00000554558.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.587

Publications

4 publications found

Variant links:

Genes affected

KTN1-AS1 (HGNC:19842): (KTN1 antisense RNA 1)

KTN1-AS1 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=-0.99).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
KTN1-AS1	ENST00000554558.6 link	n.388-18801C>T	intron_variant	Intron 3 of 3	4
KTN1-AS1	ENST00000663990.1 link	n.377-2677C>T	intron_variant	Intron 3 of 3
KTN1-AS1	ENST00000743879.1 link	n.389-621C>T	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.578

AC:

87889

AN:

151974

Hom.:

26076

Cov.:

show subpopulations

Gnomad AFR

AF:

0.467

Gnomad AMI

AF:

0.764

Gnomad AMR

AF:

0.574

Gnomad ASJ

AF:

0.629

Gnomad EAS

AF:

0.433

Gnomad SAS

AF:

0.512

Gnomad FIN

AF:

0.600

Gnomad MID

AF:

0.576

Gnomad NFE

AF:

0.654

Gnomad OTH

AF:

0.595

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.578

AC:

87922

AN:

152092

Hom.:

26080

Cov.:

AF XY:

0.574

AC XY:

42712

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.467

AC:

19352

AN:

41474

American (AMR)

AF:

0.573

AC:

8760

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.629

AC:

2180

AN:

3468

East Asian (EAS)

AF:

0.432

AC:

2235

AN:

5168

South Asian (SAS)

AF:

0.513

AC:

2474

AN:

4826

European-Finnish (FIN)

AF:

0.600

AC:

6342

AN:

10564

Middle Eastern (MID)

AF:

0.571

AC:

168

AN:

294

European-Non Finnish (NFE)

AF:

0.654

AC:

44468

AN:

67992

Other (OTH)

AF:

0.590

AC:

1248

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1910

3819

5729

7638

9548

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

744

1488

2232

2976

3720

<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:

0.629

Hom.:

28397

Bravo

AF:

0.567

Asia WGS

AF:

0.461

AC:

1606

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.4

(source)

DANN

Benign

0.28

PhyloP100

-0.59

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