Genetic Variant ENST00000815517.1:n.220-1062_220-1061insTG (chr17-41059237-A-ATG) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000815517.1(ENSG00000306126):n.220-1062_220-1061insTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 176,298 control chromosomes in the GnomAD database, including 3,787 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.12 ( 3723 hom., cov: 30)

Exomes 𝑓: 0.015 ( 64 hom. )

Consequence

ENSG00000306126
ENST00000815517.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.185

Publications

1 publications found

Variant links:

Genes affected

ENSG00000306126 (HGNC:):

ENSG00000306126 links:

KRTAP2-3 (HGNC:18906): (keratin associated protein 2-3) Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

KRTAP2-3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KRTAP2-3	NM_001165252.2 link	c.426_427insCA		downstream_gene_variant		ENST00000391418.3	NP_001158724.1	P0C7H8Q9BYR9

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ENSG00000306126	ENST00000815517.1 link	n.220-1062_220-1061insTG	intron_variant	Intron 2 of 2
ENSG00000306126	ENST00000815518.1 link	n.160-1062_160-1061insTG	intron_variant	Intron 1 of 1
ENSG00000306126	ENST00000815519.1 link	n.333-1062_333-1061insTG	intron_variant	Intron 2 of 2
KRTAP2-3	ENST00000391418.3 link	c.426_427insCA	downstream_gene_variant		6	NM_001165252.2	ENSP00000375237.2	P0C7H8

Frequencies

GnomAD3 genomes

AF:

0.119

AC:

18078

AN:

151382

Hom.:

3709

Cov.:

show subpopulations

Gnomad AFR

AF:

0.416

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0420

Gnomad ASJ

AF:

0.00231

Gnomad EAS

AF:

0.00289

Gnomad SAS

AF:

0.00417

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.00174

Gnomad OTH

AF:

0.0809

GnomAD4 exome

AF:

0.0146

AC:

362

AN:

24798

Hom.:

Cov.:

AF XY:

0.0129

AC XY:

159

AN XY:

12332

show subpopulations

African (AFR)

AF:

0.373

AC:

277

AN:

742

American (AMR)

AF:

0.0123

AC:

AN:

1630

Ashkenazi Jewish (ASJ)

AF:

0.00126

AC:

AN:

796

East Asian (EAS)

AF:

0.00189

AC:

AN:

1056

South Asian (SAS)

AF:

0.00181

AC:

AN:

552

European-Finnish (FIN)

AF:

0.00115

AC:

AN:

872

Middle Eastern (MID)

AF:

0.0156

AC:

AN:

128

European-Non Finnish (NFE)

AF:

0.000857

AC:

AN:

17502

Other (OTH)

AF:

0.0283

AC:

AN:

1520

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.120

AC:

18139

AN:

151500

Hom.:

3723

Cov.:

AF XY:

0.116

AC XY:

8564

AN XY:

74096

show subpopulations

African (AFR)

AF:

0.417

AC:

17171

AN:

41208

American (AMR)

AF:

0.0419

AC:

636

AN:

15170

Ashkenazi Jewish (ASJ)

AF:

0.00231

AC:

AN:

3464

East Asian (EAS)

AF:

0.00289

AC:

AN:

5186

South Asian (SAS)

AF:

0.00376

AC:

AN:

4792

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10572

Middle Eastern (MID)

AF:

0.0170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00174

AC:

118

AN:

67806

Other (OTH)

AF:

0.0801

AC:

168

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

544

1089

1633

2178

2722

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

148

296

444

592

740

<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:

0.109

Hom.:

259

Bravo

AF:

0.138

Asia WGS

AF:

0.0270

AC:

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.18

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