rs6848312

chr4-6834935-A-C

Variant summary

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

The NM_014743.3(KIAA0232):c.232-7132A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,158 control chromosomes in the GnomAD database, including 1,134 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 0.11 (1134 hom., cov: 32)
• Consequence: KIAA0232 NM_014743.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391

Genes affected

KIAA0232 (HGNC:28992): (KIAA0232) Predicted to enable ATP binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA0232	NM_014743.3	c.232-7132A>C		intron_variant		ENST00000307659.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA0232	ENST00000307659.6	c.232-7132A>C		intron_variant		1	NM_014743.3	P1
KIAA0232	ENST00000425103.5	c.232-7132A>C		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16290 AN: 152040 Hom.: 1134 Cov.: 32

Gnomad AFR AF: 0.0610

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0710

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0189

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.0876

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

GnomAD4 genome AF: 0.107 AC: 16293 AN: 152158 Hom.: 1134 Cov.: 32 AF XY: 0.112 AC XY: 8298 AN XY: 74380

Gnomad4 AFR AF: 0.0609

Gnomad4 AMR AF: 0.0708

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.0185

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.0877

Alfa AF: 0.121 Hom.: 1493

Bravo AF: 0.0917

Asia WGS AF: 0.0820 AC: 283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.5
Dann	Benign	0.50

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: rs6848312; hg19: chr4-6836662;