rs9314105

Positions:

• chr5-94307411-G-A
• chr5-94307411-G-C
• chr5-94307411-G-T

Variant summary

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

The NM_001145678.3(KIAA0825):​c.3710+76957C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,260 control chromosomes in the GnomAD database, including 11,622 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 0.39 (11622 hom., cov: 31)
• Consequence: KIAA0825 NM_001145678.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900

Genes affected

KIAA0825 (HGNC:28532): (KIAA0825)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA0825	NM_001145678.3	c.3710+76957C>T		intron_variant		ENST00000682413.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA0825	ENST00000682413.1	c.3710+76957C>T		intron_variant			NM_001145678.3	A1
KIAA0825	ENST00000513200.7	c.3710+76957C>T		intron_variant		5		A1
KIAA0825	ENST00000703867.1	c.3725+76957C>T		intron_variant				P4

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58318 AN: 151138 Hom.: 11588 Cov.: 31

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.365

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.386 AC: 58414 AN: 151260 Hom.: 11622 Cov.: 31 AF XY: 0.384 AC XY: 28380 AN XY: 73892

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.407

Alfa AF: 0.332 Hom.: 2190

Bravo AF: 0.376

Asia WGS AF: 0.338 AC: 1177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.1
DANN	Benign	0.58

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9314105; hg19: chr5-93643116;