rs1993912

Positions:

• chr9-5987781-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001017969.3(KIAA2026):​c.794+564T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0509 in 152,264 control chromosomes in the GnomAD database, including 331 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 0.051 (331 hom., cov: 32)
• Consequence: KIAA2026 NM_001017969.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201

Genes affected

KIAA2026 (HGNC:23378): (bromodomain containing 10)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA2026	NM_001017969.3	c.794+564T>G		intron_variant		ENST00000399933.8	NP_001017969.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIAA2026	ENST00000399933.8	c.794+564T>G		intron_variant		5	NM_001017969.3	ENSP00000382815	P4
KIAA2026	ENST00000381461.6	c.794+564T>G		intron_variant		5		ENSP00000370870	A2
KIAA2026	ENST00000513355.2	c.594-18345T>G		intron_variant		5		ENSP00000444993

Frequencies

GnomAD3 genomes AF: 0.0509 AC: 7738 AN: 152146 Hom.: 327 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.0725

Gnomad AMR AF: 0.0240

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.0239

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0400

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0173

Gnomad OTH AF: 0.0382

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

GnomAD4 genome AF: 0.0509 AC: 7752 AN: 152264 Hom.: 331 Cov.: 32 AF XY: 0.0529 AC XY: 3940 AN XY: 74454

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.0239

Gnomad4 ASJ AF: 0.0101

Gnomad4 EAS AF: 0.0237

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.0400

Gnomad4 NFE AF: 0.0173

Gnomad4 OTH AF: 0.0445

Alfa AF: 0.0278 Hom.: 67

Bravo AF: 0.0509

Asia WGS AF: 0.102 AC: 355 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.0
DANN	Benign	0.69

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: rs1993912; hg19: chr9-5987781;