Genetic Variant KRTAP5-AS1:n.1710C>A (chr11-1598629-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000424148.1(KRTAP5-AS1):n.1710C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 364,414 control chromosomes in the GnomAD database, including 5,152 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 0.18 ( 2624 hom., cov: 31)

Exomes 𝑓: 0.14 ( 2528 hom. )

Consequence

KRTAP5-AS1
ENST00000424148.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.08

Publications

8 publications found

Variant links:

Genes affected

KRTAP5-AS1 (HGNC:27877): (KRTAP5-1/KRTAP5-2 antisense RNA 1)

KRTAP5-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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KRTAP5-AS1	NR_021489.2 link	n.1710C>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KRTAP5-AS1	ENST00000424148.1 link	n.1710C>A		non_coding_transcript_exon_variant	Exon 2 of 2	2
KRTAP5-AS1	ENST00000792906.1 link	n.214-13736C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.177

AC:

26915

AN:

152056

Hom.:

2619

Cov.:

show subpopulations

Gnomad AFR

AF:

0.258

Gnomad AMI

AF:

0.218

Gnomad AMR

AF:

0.143

Gnomad ASJ

AF:

0.248

Gnomad EAS

AF:

0.117

Gnomad SAS

AF:

0.154

Gnomad FIN

AF:

0.106

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.148

Gnomad OTH

AF:

0.167

GnomAD4 exome

AF:

0.145

AC:

30773

AN:

212240

Hom.:

2528

Cov.:

AF XY:

0.147

AC XY:

16408

AN XY:

111272

show subpopulations

African (AFR)

AF:

0.248

AC:

1706

AN:

6882

American (AMR)

AF:

0.116

AC:

1038

AN:

8954

Ashkenazi Jewish (ASJ)

AF:

0.204

AC:

1292

AN:

6340

East Asian (EAS)

AF:

0.105

AC:

1292

AN:

12304

South Asian (SAS)

AF:

0.167

AC:

4329

AN:

25918

European-Finnish (FIN)

AF:

0.108

AC:

1218

AN:

11306

Middle Eastern (MID)

AF:

0.211

AC:

191

AN:

904

European-Non Finnish (NFE)

AF:

0.140

AC:

17878

AN:

127698

Other (OTH)

AF:

0.153

AC:

1829

AN:

11934

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

Heterozygous variant carriers

1231

2462

3692

4923

6154

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

162

324

486

648

810

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.177

AC:

26959

AN:

152174

Hom.:

2624

Cov.:

AF XY:

0.173

AC XY:

12861

AN XY:

74398

show subpopulations

African (AFR)

AF:

0.259

AC:

10738

AN:

41514

American (AMR)

AF:

0.143

AC:

2189

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.248

AC:

860

AN:

3468

East Asian (EAS)

AF:

0.117

AC:

604

AN:

5176

South Asian (SAS)

AF:

0.154

AC:

740

AN:

4816

European-Finnish (FIN)

AF:

0.106

AC:

1127

AN:

10594

Middle Eastern (MID)

AF:

0.201

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.148

AC:

10091

AN:

67990

Other (OTH)

AF:

0.167

AC:

353

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1115

2231

3346

4462

5577

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

276

552

828

1104

1380

<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:

0.151

Hom.:

3802

Bravo

AF:

0.183

Asia WGS

AF:

0.186

AC:

648

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.45

(source)

DANN

Benign

0.79

PhyloP100

-2.1

PromoterAI

0.00010

Neutral

(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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over