rs7606048

chr2-23411340-C-T

Variant summary

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

The NM_052920.2(KLHL29):c.-154+25560C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.767 in 150,708 control chromosomes in the GnomAD database, including 44,500 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 0.77 (44500 hom., cov: 26)
• Consequence: KLHL29 NM_052920.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KLHL29	NM_052920.2	c.-154+25560C>T		intron_variant		ENST00000486442.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KLHL29	ENST00000486442.6	c.-154+25560C>T		intron_variant		5	NM_052920.2	P1

Frequencies

GnomAD3 genomes AF: 0.767 AC: 115444 AN: 150590 Hom.: 44438 Cov.: 26

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.767 AC: 115568 AN: 150708 Hom.: 44500 Cov.: 26 AF XY: 0.767 AC XY: 56393 AN XY: 73478

Gnomad4 AFR AF: 0.831

Gnomad4 AMR AF: 0.763

Gnomad4 ASJ AF: 0.692

Gnomad4 EAS AF: 0.724

Gnomad4 SAS AF: 0.854

Gnomad4 FIN AF: 0.784

Gnomad4 NFE AF: 0.729

Gnomad4 OTH AF: 0.750

Alfa AF: 0.749 Hom.: 11962

Bravo AF: 0.765

Asia WGS AF: 0.836 AC: 2907 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.6
Dann	Benign	0.25

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: rs7606048; hg19: chr2-23634211;