rs9939606

Variant names:

• chr16-85056770-G-A
• rs9939606
• NM_001388359.1:c.-172-10130G>A

Variant summary

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

The NM_001388359.1(KIAA0513):​c.-172-10130G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0726 in 152,256 control chromosomes in the GnomAD database, including 414 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 0.073 (414 hom., cov: 33)
• Consequence: KIAA0513 NM_001388359.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 9 publications found

Genes affected

KIAA0513 (HGNC:29058): (KIAA0513) Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000299192 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA0513	NM_001388359.1	c.-172-10130G>A		intron_variant	Intron 1 of 12	ENST00000683363.1	NP_001375288.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA0513	ENST00000683363.1	c.-172-10130G>A		intron_variant	Intron 1 of 12		NM_001388359.1	ENSP00000507772.1
KIAA0513	ENST00000567328.6	c.-172-10130G>A		intron_variant	Intron 1 of 7	1		ENSP00000455544.1
KIAA0513	ENST00000538274.6	c.-172-10130G>A		intron_variant	Intron 1 of 11	2		ENSP00000446439.1
ENSG00000299192	ENST00000761486.1	n.264-615G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0726 AC: 11041 AN: 152138 Hom.: 413 Cov.: 33

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0453

Gnomad ASJ AF: 0.0455

Gnomad EAS AF: 0.0542

Gnomad SAS AF: 0.0667

Gnomad FIN AF: 0.0641

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0651

Gnomad OTH AF: 0.0660

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

GnomAD4 genome AF: 0.0726 AC: 11054 AN: 152256 Hom.: 414 Cov.: 33 AF XY: 0.0721 AC XY: 5367 AN XY: 74464

African (AFR) AF: 0.104 AC: 4326 AN: 41540

American (AMR) AF: 0.0452 AC: 691 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0455 AC: 158 AN: 3470

East Asian (EAS) AF: 0.0542 AC: 281 AN: 5188

South Asian (SAS) AF: 0.0667 AC: 322 AN: 4826

European-Finnish (FIN) AF: 0.0641 AC: 681 AN: 10618

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0652 AC: 4433 AN: 68008

Other (OTH) AF: 0.0676 AC: 143 AN: 2114

Alfa AF: 0.0731 Hom.: 50

Bravo AF: 0.0720

Asia WGS AF: 0.0790 AC: 276 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	3.2
DANN	Benign	0.52
PhyloP100		0.36
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: rs9939606; hg19: chr16-85090376;