rs11884397

Positions:

• chr2-23662518-G-A

Variant summary

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

The NM_052920.2(KLHL29):​c.940+19668G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,178 control chromosomes in the GnomAD database, including 924 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 0.10 (924 hom., cov: 33)
• Consequence: KLHL29 NM_052920.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KLHL29	NM_052920.2	c.940+19668G>A		intron_variant		ENST00000486442.6
KLHL29	XM_006711929.4	c.940+19668G>A		intron_variant
KLHL29	XM_011532501.3	c.22+17414G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KLHL29	ENST00000486442.6	c.940+19668G>A		intron_variant		5	NM_052920.2	P1
KLHL29	ENST00000288548.5	c.459+19668G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15543 AN: 152060 Hom.: 922 Cov.: 33

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0608

Gnomad ASJ AF: 0.0764

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0824

Gnomad OTH AF: 0.0851

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

GnomAD4 genome AF: 0.102 AC: 15552 AN: 152178 Hom.: 924 Cov.: 33 AF XY: 0.105 AC XY: 7826 AN XY: 74412

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.0606

Gnomad4 ASJ AF: 0.0764

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.0823

Gnomad4 OTH AF: 0.0847

Alfa AF: 0.0887 Hom.: 323

Bravo AF: 0.0954

Asia WGS AF: 0.152 AC: 530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.29
DANN	Benign	0.82

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: rs11884397; hg19: chr2-23885388;