Genetic Variant KLHL32:c.-653_-652insAGCA (chr6-97010244-G-GAAGC) – ACMG Classification: Benign (-8 pts)

Variant summary

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

The NM_001323263.2(KLHL32):c.-9_-8insAGCA variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.65 ( 33894 hom., cov: 0)

Exomes 𝑓: 0.70 ( 5 hom. )

Consequence

KLHL32
NM_001323263.2 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.04

Publications

4 publications found

Variant links:

Genes affected

KLHL32 (HGNC:21221): (kelch like family member 32)

KLHL32 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 = 0.883 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001323263.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
KLHL32	NM_052904.4	MANE Select	c.205-31247_205-31246insAGCA	intron	N/A	NP_443136.2	Q96NJ5-1
KLHL32	NM_001323263.2		c.-9_-8insAGCA	5_prime_UTR	Exon 1 of 9	NP_001310192.1
KLHL32	NM_001323264.2		c.-9_-8insAGCA	5_prime_UTR	Exon 1 of 8	NP_001310193.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
KLHL32	ENST00000620278.1	TSL:1	c.-653_-652insAGCA	5_prime_UTR	Exon 1 of 9	ENSP00000482012.1	A0A087WYQ8
KLHL32	ENST00000369261.9	TSL:2 MANE Select	c.205-31247_205-31246insAGCA	intron	N/A	ENSP00000358265.4	Q96NJ5-1
KLHL32	ENST00000951639.1		c.205-31247_205-31246insAGCA	intron	N/A	ENSP00000621698.1

Frequencies

GnomAD3 genomes

AF:

0.650

AC:

98384

AN:

151358

Hom.:

33834

Cov.:

show subpopulations

Gnomad AFR

AF:

0.890

Gnomad AMI

AF:

0.483

Gnomad AMR

AF:

0.671

Gnomad ASJ

AF:

0.577

Gnomad EAS

AF:

0.601

Gnomad SAS

AF:

0.697

Gnomad FIN

AF:

0.523

Gnomad MID

AF:

0.580

Gnomad NFE

AF:

0.526

Gnomad OTH

AF:

0.636

GnomAD4 exome

AF:

0.700

AC:

AN:

Hom.:

Cov.:

AF XY:

0.667

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.833

AC:

AN:

Other (OTH)

AF:

0.750

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.438

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

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:

0.650

AC:

98505

AN:

151474

Hom.:

33894

Cov.:

AF XY:

0.651

AC XY:

48175

AN XY:

73960

show subpopulations

African (AFR)

AF:

0.890

AC:

36784

AN:

41322

American (AMR)

AF:

0.672

AC:

10241

AN:

15240

Ashkenazi Jewish (ASJ)

AF:

0.577

AC:

1997

AN:

3462

East Asian (EAS)

AF:

0.600

AC:

3082

AN:

5134

South Asian (SAS)

AF:

0.696

AC:

3341

AN:

4798

European-Finnish (FIN)

AF:

0.523

AC:

5447

AN:

10412

Middle Eastern (MID)

AF:

0.579

AC:

169

AN:

292

European-Non Finnish (NFE)

AF:

0.526

AC:

35671

AN:

67810

Other (OTH)

AF:

0.636

AC:

1334

AN:

2096

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

1567

3134

4701

6268

7835

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

764

1528

2292

3056

3820

<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:

0.572

Hom.:

2737

Asia WGS

AF:

0.701

AC:

2439

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over