rs5924066

Variant names:

• chrX-87617650-C-A
• rs5924066
• NM_019117.5:c.728-282C>A

Your query was ambiguous. Multiple possible variants found:

• chrX-87617650-C-A
• chrX-87617650-C-G
• chrX-87617650-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_019117.5(KLHL4):​c.728-282C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 23)
• Consequence: KLHL4 NM_019117.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240

Genes affected

KLHL4 (HGNC:6355): (kelch like family member 4) This gene encodes a member of the kelch family of proteins, which are characterized by kelch repeat motifs and a POZ/BTB protein-binding domain. It is thought that kelch repeats are actin binding domains. However, the specific function of this protein has not been determined. Alternative splicing of this gene results in two transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KLHL4	NM_019117.5	c.728-282C>A		intron_variant	Intron 3 of 10	ENST00000373119.9	NP_061990.2
KLHL4	NM_057162.3	c.728-282C>A		intron_variant	Intron 3 of 10		NP_476503.1
KLHL4	XR_938403.3	n.820-282C>A		intron_variant	Intron 3 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KLHL4	ENST00000373119.9	c.728-282C>A		intron_variant	Intron 3 of 10	1	NM_019117.5	ENSP00000362211.4
KLHL4	ENST00000373114.4	c.728-282C>A		intron_variant	Intron 3 of 10	1		ENSP00000362206.4
KLHL4	ENST00000652270.1	n.728-282C>A		intron_variant	Intron 3 of 11			ENSP00000498718.1

Frequencies

GnomAD3 genomes Cov.: 23

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

GnomAD4 genome Cov.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.46

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

LitVar

Other links and lift over

dbSNP: rs5924066; hg19: chrX-86872653;