chr14-20429334-C-A

Variant names:

• chr14-20429334-C-A
• NM_001365790.2:c.1909G>T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001365790.2(KLHL33):​c.1909G>T​(p.Val637Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000715 in 1,399,414 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 7.1e-7 (0 hom.)
• Consequence: KLHL33 NM_001365790.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.680

Genes affected

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

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.2733539).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KLHL33	NM_001365790.2	c.1909G>T	p.Val637Leu	missense_variant	Exon 5 of 5	ENST00000636854.3	NP_001352719.1
KLHL33	NM_001109997.3	c.1117G>T	p.Val373Leu	missense_variant	Exon 4 of 4		NP_001103467.2
KLHL33	XM_011536450.3	c.1909G>T	p.Val637Leu	missense_variant	Exon 5 of 5		XP_011534752.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KLHL33	ENST00000636854.3	c.1909G>T	p.Val637Leu	missense_variant	Exon 5 of 5	5	NM_001365790.2	ENSP00000490040.1
KLHL33	ENST00000344581.4	c.1117G>T	p.Val373Leu	missense_variant	Exon 4 of 4	5		ENSP00000341549.4
KLHL33	ENST00000637228	c.*68G>T		3_prime_UTR_variant	Exon 4 of 4	5		ENSP00000489731.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.15e-7 AC: 1 AN: 1399414 Hom.: 0 Cov.: 37 AF XY: 0.00 AC XY: 0 AN XY: 690208

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.27e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.39
CADD	Benign	0.15
DANN	Benign	0.79
DEOGEN2	Benign	0.028	T;T
Eigen	Benign	-0.99
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.21	N
LIST_S2	Benign	0.63	T;T
M_CAP	Benign	0.051	D
MetaRNN	Benign	0.27	T;T
MetaSVM	Benign	-0.47	T
MutationAssessor	Uncertain	2.1	.;M
PrimateAI	Benign	0.36	T
PROVEAN	Benign	-1.7	.;N
REVEL	Uncertain	0.41
Sift	Benign	0.10	.;T
Sift4G	Benign	0.096	.;T
Polyphen		0.014	.;B
Vest4		0.32
MutPred		0.62		.;Gain of sheet (P = 0.0827);
MVP		0.048
ClinPred		0.35	T
GERP RS		-3.5
Varity_R		0.087
gMVP		0.42

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr14-20897493;