rs10513160

Variant names:

• chr9-112561932-A-G
• rs10513160
• NM_133465.4:c.-24-12125A>G

Variant summary

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

The NM_133465.4(KIAA1958):​c.-24-12125A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,102 control chromosomes in the GnomAD database, including 7,182 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 0.30 (7182 hom., cov: 32)
• Consequence: KIAA1958 NM_133465.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• Publications: 0 publications found

Genes affected

KIAA1958 (HGNC:23427): (KIAA1958)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA1958	NM_133465.4	c.-24-12125A>G		intron_variant	Intron 1 of 3	ENST00000337530.11	NP_597722.1
KIAA1958	NM_001287036.2	c.-24-12125A>G		intron_variant	Intron 1 of 4		NP_001273965.1
KIAA1958	NM_001287038.2	c.-24-12125A>G		intron_variant	Intron 1 of 3		NP_001273967.1
KIAA1958	XM_011518311.3	c.-24-12125A>G		intron_variant	Intron 1 of 2		XP_011516613.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA1958	ENST00000337530.11	c.-24-12125A>G		intron_variant	Intron 1 of 3	1	NM_133465.4	ENSP00000336940.6
KIAA1958	ENST00000536272.5	c.-24-12125A>G		intron_variant	Intron 1 of 4	1		ENSP00000440504.1
KIAA1958	ENST00000374244.3	c.-24-12125A>G		intron_variant	Intron 1 of 2	5		ENSP00000363362.3

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45702 AN: 151984 Hom.: 7161 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.301 AC: 45770 AN: 152102 Hom.: 7182 Cov.: 32 AF XY: 0.299 AC XY: 22205 AN XY: 74374

African (AFR) AF: 0.389 AC: 16121 AN: 41462

American (AMR) AF: 0.336 AC: 5133 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1037 AN: 3464

East Asian (EAS) AF: 0.201 AC: 1042 AN: 5176

South Asian (SAS) AF: 0.304 AC: 1467 AN: 4818

European-Finnish (FIN) AF: 0.183 AC: 1940 AN: 10584

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17931 AN: 67990

Other (OTH) AF: 0.319 AC: 674 AN: 2112

Alfa AF: 0.299 Hom.: 1048

Bravo AF: 0.315

Asia WGS AF: 0.261 AC: 911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.64
PhyloP100		1.2
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: rs10513160; hg19: chr9-115324212;