rs9372321

chr6-97045819-T-C

Variant summary

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

The NM_052904.4(KLHL32):c.312+4220T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0766 in 152,254 control chromosomes in the GnomAD database, including 466 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 0.077 (466 hom., cov: 32)
• Consequence: KLHL32 NM_052904.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

KLHL32 (HGNC:21221): (kelch like family member 32)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KLHL32	NM_052904.4	c.312+4220T>C		intron_variant		ENST00000369261.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KLHL32	ENST00000369261.9	c.312+4220T>C		intron_variant		2	NM_052904.4	P1

Frequencies

GnomAD3 genomes AF: 0.0767 AC: 11662 AN: 152136 Hom.: 468 Cov.: 32

Gnomad AFR AF: 0.0664

Gnomad AMI AF: 0.0747

Gnomad AMR AF: 0.0746

Gnomad ASJ AF: 0.0757

Gnomad EAS AF: 0.0719

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.0871

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0761

Gnomad OTH AF: 0.0890

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

GnomAD4 genome AF: 0.0766 AC: 11662 AN: 152254 Hom.: 466 Cov.: 32 AF XY: 0.0783 AC XY: 5830 AN XY: 74438

Gnomad4 AFR AF: 0.0662

Gnomad4 AMR AF: 0.0746

Gnomad4 ASJ AF: 0.0757

Gnomad4 EAS AF: 0.0719

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.0871

Gnomad4 NFE AF: 0.0761

Gnomad4 OTH AF: 0.0881

Alfa AF: 0.0734 Hom.: 78

Bravo AF: 0.0740

Asia WGS AF: 0.118 AC: 414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.81
Dann	Benign	0.71

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: rs9372321; hg19: chr6-97493695;