chr6-97045819-T-C

Variant names:

• chr6-97045819-T-C
• rs9372321
• NM_052904.4:c.312+4220T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
KLHL32	NM_052904.4	c.312+4220T>C		intron_variant	Intron 4 of 10	ENST00000369261.9	NP_443136.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KLHL32	ENST00000369261.9	c.312+4220T>C		intron_variant	Intron 4 of 10	2	NM_052904.4	ENSP00000358265.4

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

African (AFR) AF: 0.0662 AC: 2751 AN: 41540

American (AMR) AF: 0.0746 AC: 1141 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0757 AC: 263 AN: 3472

East Asian (EAS) AF: 0.0719 AC: 373 AN: 5190

South Asian (SAS) AF: 0.156 AC: 751 AN: 4826

European-Finnish (FIN) AF: 0.0871 AC: 923 AN: 10600

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0761 AC: 5177 AN: 68010

Other (OTH) AF: 0.0881 AC: 186 AN: 2112

Alfa AF: 0.0730 Hom.: 80

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
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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: rs9372321; hg19: chr6-97493695;