rs4665630

chr2-23675447-C-Achr2-23675447-C-Gchr2-23675447-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_052920.2(KLHL29):c.941-8952C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: 32)
• Consequence: KLHL29 NM_052920.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.562

Genes affected

KLHL29 (HGNC:29404): (kelch like family member 29)

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KLHL29	NM_052920.2	c.941-8952C>A		intron_variant		ENST00000486442.6
KLHL29	XM_006711929.4	c.941-8952C>A		intron_variant
KLHL29	XM_011532501.3	c.23-8952C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KLHL29	ENST00000486442.6	c.941-8952C>A		intron_variant		5	NM_052920.2	P1
KLHL29	ENST00000288548.5	c.460-8952C>A		intron_variant		1
	ENST00000634300.1	n.163-2641G>T		intron_variant, non_coding_transcript_variant		5
	ENST00000655321.1	n.163-2641G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	6.7
Dann	Benign	0.60

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: rs4665630; hg19: chr2-23898317;