rs6007503

chr22-45214492-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

KIAA0930 (HGNC:1314): (KIAA0930)

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA0930	NM_001009880.2	c.65-2385T>C		intron_variant		ENST00000336156.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA0930	ENST00000336156.10	c.65-2385T>C		intron_variant		1	NM_001009880.2

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

Gnomad4 AFR AF: 0.0918

Gnomad4 AMR AF: 0.0616

Gnomad4 ASJ AF: 0.0841

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.0781

Gnomad4 FIN AF: 0.0650

Gnomad4 NFE AF: 0.0947

Gnomad4 OTH AF: 0.100

Alfa AF: 0.0955 Hom.: 1440

Bravo AF: 0.0926

Asia WGS AF: 0.117 AC: 405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.40
Dann	Benign	0.12

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: rs6007503; hg19: chr22-45610373;