22-45214492-A-G

Variant names:

• chr22-45214492-A-G
• rs6007503
• NM_001009880.2:c.65-2385T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001009880.2(KIAA0930):​c.65-2385T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0915 in 152,316 control chromosomes in the GnomAD database, including 694 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 0.092 (694 hom., cov: 33)
• Consequence: KIAA0930 NM_001009880.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.19
• Publications: 2 publications found

Genes affected

KIAA0930 (HGNC:1314): (KIAA0930)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.1).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001009880.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA0930	NM_001009880.2	MANE Select	c.65-2385T>C		intron	N/A	NP_001009880.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA0930	ENST00000336156.10	TSL:1 MANE Select	c.65-2385T>C		intron	N/A	ENSP00000336720.4
	KIAA0930	ENST00000391627.6	TSL:1	c.-38-2385T>C		intron	N/A	ENSP00000375485.2
	KIAA0930	ENST00000927183.1		c.65-2385T>C		intron	N/A	ENSP00000597242.1

Frequencies

GnomAD3 genomes AF: 0.0916 AC: 13934 AN: 152198 Hom.: 694 Cov.: 33

Gnomad AFR AF: 0.0918

Gnomad AMI AF: 0.0978

Gnomad AMR AF: 0.0617

Gnomad ASJ AF: 0.0841

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.0793

Gnomad FIN AF: 0.0650

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.0947

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0915 AC: 13938 AN: 152316 Hom.: 694 Cov.: 33 AF XY: 0.0903 AC XY: 6722 AN XY: 74476

African (AFR) AF: 0.0918 AC: 3816 AN: 41562

American (AMR) AF: 0.0616 AC: 943 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0841 AC: 292 AN: 3470

East Asian (EAS) AF: 0.202 AC: 1045 AN: 5182

South Asian (SAS) AF: 0.0781 AC: 377 AN: 4828

European-Finnish (FIN) AF: 0.0650 AC: 690 AN: 10616

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.0947 AC: 6446 AN: 68038

Other (OTH) AF: 0.100 AC: 212 AN: 2112

Alfa AF: 0.0952 Hom.: 2943

Bravo AF: 0.0926

Asia WGS AF: 0.117 AC: 405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.40
DANN	Benign	0.12
PhyloP100		-4.2
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: rs6007503; hg19: chr22-45610373;