rs10739367

Variant names:

• chr9-112604798-C-T
• rs10739367
• NM_133465.4:c.1171+29547C>T

Variant summary

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

The NM_133465.4(KIAA1958):​c.1171+29547C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 151,234 control chromosomes in the GnomAD database, including 20,553 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 0.52 (20553 hom., cov: 31)
• Consequence: KIAA1958 NM_133465.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.936
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_133465.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1958	NM_133465.4	MANE Select	c.1171+29547C>T		intron	N/A	NP_597722.1
	KIAA1958	NM_001287036.2		c.1172-13073C>T		intron	N/A	NP_001273965.1
	KIAA1958	NM_001287038.2		c.1171+29547C>T		intron	N/A	NP_001273967.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1958	ENST00000337530.11	TSL:1 MANE Select	c.1171+29547C>T		intron	N/A	ENSP00000336940.6
	KIAA1958	ENST00000536272.5	TSL:1	c.1172-13073C>T		intron	N/A	ENSP00000440504.1
	KIAA1958	ENST00000374244.3	TSL:5	c.1172-13073C>T		intron	N/A	ENSP00000363362.3

Frequencies

GnomAD3 genomes AF: 0.520 AC: 78558 AN: 151136 Hom.: 20546 Cov.: 31

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.520 AC: 78591 AN: 151234 Hom.: 20553 Cov.: 31 AF XY: 0.521 AC XY: 38488 AN XY: 73904

African (AFR) AF: 0.446 AC: 18401 AN: 41292

American (AMR) AF: 0.513 AC: 7786 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1761 AN: 3466

East Asian (EAS) AF: 0.479 AC: 2469 AN: 5154

South Asian (SAS) AF: 0.547 AC: 2630 AN: 4806

European-Finnish (FIN) AF: 0.584 AC: 5969 AN: 10218

Middle Eastern (MID) AF: 0.449 AC: 131 AN: 292

European-Non Finnish (NFE) AF: 0.558 AC: 37867 AN: 67832

Other (OTH) AF: 0.492 AC: 1032 AN: 2098

Alfa AF: 0.542 Hom.: 37885

Bravo AF: 0.509

Asia WGS AF: 0.513 AC: 1781 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.53
DANN	Benign	0.65
PhyloP100		-0.94
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: rs10739367; hg19: chr9-115367078;