dbSNP rs7140768: KLHL33:c.*151G>A (chr14-20428698-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001365790.2(KLHL33):c.*151G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 717,230 control chromosomes in the GnomAD database, including 121,551 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 ( 25386 hom., cov: 33)

Exomes 𝑓: 0.58 ( 96165 hom. )

Consequence

KLHL33
NM_001365790.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.997

Variant links:

Genes affected

KLHL33 (HGNC:31952): (kelch like family member 33)

KLHL33 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
KLHL33	NM_001365790.2 link	c.*151G>A	3_prime_UTR_variant	Exon 5 of 5	ENST00000636854.3	NP_001352719.1
KLHL33	NM_001109997.3 link	c.*151G>A	3_prime_UTR_variant	Exon 4 of 4		NP_001103467.2	A6NCF5B2RUZ8
KLHL33	XM_011536450.3 link	c.*151G>A	3_prime_UTR_variant	Exon 5 of 5		XP_011534752.1	A0A1B0GUB7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
KLHL33	ENST00000636854 link	c.*151G>A	3_prime_UTR_variant	Exon 5 of 5	5	NM_001365790.2	ENSP00000490040.1	A0A1B0GUB7
KLHL33	ENST00000637228 link	c.*704G>A	3_prime_UTR_variant	Exon 4 of 4	5		ENSP00000489731.1	A0A1B0GTK0
KLHL33	ENST00000344581.4 link	c.*151G>A	downstream_gene_variant		5		ENSP00000341549.4	A6NCF5

Frequencies

GnomAD3 genomes

AF:

0.578

AC:

87819

AN:

152036

Hom.:

25349

Cov.:

show subpopulations

Gnomad AFR

AF:

0.572

Gnomad AMI

AF:

0.644

Gnomad AMR

AF:

0.534

Gnomad ASJ

AF:

0.578

Gnomad EAS

AF:

0.607

Gnomad SAS

AF:

0.691

Gnomad FIN

AF:

0.602

Gnomad MID

AF:

0.650

Gnomad NFE

AF:

0.575

Gnomad OTH

AF:

0.608

GnomAD4 exome

AF:

0.581

AC:

328073

AN:

565076

Hom.:

96165

Cov.:

AF XY:

0.585

AC XY:

169481

AN XY:

289864

show subpopulations

Gnomad4 AFR exome

AF:

0.569

Gnomad4 AMR exome

AF:

0.504

Gnomad4 ASJ exome

AF:

0.598

Gnomad4 EAS exome

AF:

0.585

Gnomad4 SAS exome

AF:

0.672

Gnomad4 FIN exome

AF:

0.591

Gnomad4 NFE exome

AF:

0.570

Gnomad4 OTH exome

AF:

0.587

GnomAD4 genome

AF:

0.578

AC:

87914

AN:

152154

Hom.:

25386

Cov.:

AF XY:

0.581

AC XY:

43195

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.572

Gnomad4 AMR

AF:

0.534

Gnomad4 ASJ

AF:

0.578

Gnomad4 EAS

AF:

0.606

Gnomad4 SAS

AF:

0.692

Gnomad4 FIN

AF:

0.602

Gnomad4 NFE

AF:

0.575

Gnomad4 OTH

AF:

0.609

Alfa

AF:

0.579

Hom.:

32995

Bravo

AF:

0.571

Asia WGS

AF:

0.617

AC:

2146

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.53

DANN

Benign

0.73

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over