Genetic Variant KLHL2P1:n.119365628G>C (chr4-119365628-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 variant allele was found at a frequency of 0.31 in 152,002 control chromosomes in the GnomAD database, including 7,468 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 0.31 ( 7468 hom., cov: 32)

Consequence

KLHL2P1
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.112

Publications

5 publications found

Variant links:

Genes affected

KLHL2P1 (HGNC:44046): (kelch like family member 2 pseudogene 1)

KLHL2P1 links:

ENSG00000294020 (HGNC:):

ENSG00000294020 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 (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KLHL2P1		n.119365628G>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
KLHL2P1	ENST00000508691.1 link	n.354+11397G>C	intron_variant	Intron 3 of 3	6
ENSG00000294020	ENST00000720595.1 link	n.530+11397G>C	intron_variant	Intron 4 of 5
ENSG00000294020	ENST00000720596.1 link	n.578+11397G>C	intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes

AF:

0.310

AC:

47103

AN:

151884

Hom.:

7465

Cov.:

show subpopulations

Gnomad AFR

AF:

0.277

Gnomad AMI

AF:

0.282

Gnomad AMR

AF:

0.293

Gnomad ASJ

AF:

0.213

Gnomad EAS

AF:

0.443

Gnomad SAS

AF:

0.245

Gnomad FIN

AF:

0.315

Gnomad MID

AF:

0.266

Gnomad NFE

AF:

0.333

Gnomad OTH

AF:

0.319

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

GnomAD4 genome

AF:

0.310

AC:

47125

AN:

152002

Hom.:

7468

Cov.:

AF XY:

0.308

AC XY:

22872

AN XY:

74266

show subpopulations

African (AFR)

AF:

0.277

AC:

11498

AN:

41468

American (AMR)

AF:

0.293

AC:

4468

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.213

AC:

740

AN:

3470

East Asian (EAS)

AF:

0.443

AC:

2284

AN:

5156

South Asian (SAS)

AF:

0.244

AC:

1178

AN:

4820

European-Finnish (FIN)

AF:

0.315

AC:

3320

AN:

10548

Middle Eastern (MID)

AF:

0.259

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.333

AC:

22636

AN:

67966

Other (OTH)

AF:

0.317

AC:

668

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1629

3257

4886

6514

8143

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

482

964

1446

1928

2410

<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:

0.301

Hom.:

897

Bravo

AF:

0.314

Asia WGS

AF:

0.311

AC:

1081

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

6.0

(source)

DANN

Benign

0.55

PhyloP100

0.11

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