rs4665609

chr2-23551882-A-Cchr2-23551882-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_052920.2(KLHL29):c.-45-10270A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 152,170 control chromosomes in the GnomAD database, including 24,969 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 0.57 (24969 hom., cov: 34)
• Consequence: KLHL29 NM_052920.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KLHL29	NM_052920.2	c.-45-10270A>C		intron_variant		ENST00000486442.6
KLHL29	XM_006711929.4	c.-45-10270A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KLHL29	ENST00000486442.6	c.-45-10270A>C		intron_variant		5	NM_052920.2	P1
KLHL29	ENST00000489446.1	n.37-10270A>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86596 AN: 152052 Hom.: 24946 Cov.: 34

Gnomad AFR AF: 0.600

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.570 AC: 86681 AN: 152170 Hom.: 24969 Cov.: 34 AF XY: 0.574 AC XY: 42676 AN XY: 74398

Gnomad4 AFR AF: 0.601

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.640

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.577

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.559

Alfa AF: 0.556 Hom.: 38340

Bravo AF: 0.567

Asia WGS AF: 0.458 AC: 1594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.84
Dann	Benign	0.68

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: rs4665609; hg19: chr2-23774752;