rs6848312

Variant names:

• chr4-6834935-A-C
• rs6848312
• NM_014743.3:c.232-7132A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
KIAA0232	NM_014743.3	c.232-7132A>C		intron_variant	Intron 3 of 9	ENST00000307659.6	NP_055558.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA0232	ENST00000307659.6	c.232-7132A>C		intron_variant	Intron 3 of 9	1	NM_014743.3	ENSP00000303928.5
KIAA0232	ENST00000425103.5	c.232-7132A>C		intron_variant	Intron 2 of 8	1		ENSP00000413739.1

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

African (AFR) AF: 0.0609 AC: 2530 AN: 41524

American (AMR) AF: 0.0708 AC: 1082 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 391 AN: 3472

East Asian (EAS) AF: 0.0185 AC: 96 AN: 5186

South Asian (SAS) AF: 0.120 AC: 580 AN: 4824

European-Finnish (FIN) AF: 0.236 AC: 2496 AN: 10570

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8859 AN: 67982

Other (OTH) AF: 0.0877 AC: 185 AN: 2110

Alfa AF: 0.118 Hom.: 1826

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
PhyloP100		-0.39
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: rs6848312; hg19: chr4-6836662;