rs4665630

Variant names:

• chr2-23675447-C-A
• rs4665630
• NM_052920.2:c.941-8952C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-23675447-C-A
• chr2-23675447-C-G
• chr2-23675447-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_052920.2(KLHL29):​c.941-8952C>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: 32)
• Consequence: KLHL29 NM_052920.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.562
• Publications: 14 publications found

Genes affected

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

ENSG00000283031 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KLHL29	NM_052920.2	c.941-8952C>A		intron_variant	Intron 5 of 13	ENST00000486442.6	NP_443152.1
KLHL29	XM_006711929.4	c.941-8952C>A		intron_variant	Intron 4 of 12		XP_006711992.1
KLHL29	XM_011532501.3	c.23-8952C>A		intron_variant	Intron 2 of 10		XP_011530803.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KLHL29	ENST00000486442.6	c.941-8952C>A		intron_variant	Intron 5 of 13	5	NM_052920.2	ENSP00000420659.1
KLHL29	ENST00000288548.5	c.458-8952C>A		intron_variant	Intron 1 of 6	1		ENSP00000288548.5
ENSG00000283031	ENST00000634300.1	n.163-2641G>T		intron_variant	Intron 1 of 6	5
ENSG00000283031	ENST00000655321.1	n.163-2641G>T		intron_variant	Intron 1 of 5

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
PhyloP100		0.56

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

Other links and lift over

dbSNP: rs4665630; hg19: chr2-23898317;