rs6869388

chr5-94474503-T-C

Variant summary

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

The NM_001145678.3(KIAA0825):c.1228-984A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 152,044 control chromosomes in the GnomAD database, including 6,094 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 0.26 (6094 hom., cov: 32)
• Consequence: KIAA0825 NM_001145678.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA0825	NM_001145678.3	c.1228-984A>G		intron_variant		ENST00000682413.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA0825	ENST00000682413.1	c.1228-984A>G		intron_variant			NM_001145678.3	A1
KIAA0825	ENST00000504117.1	n.75-984A>G		intron_variant, non_coding_transcript_variant		1
KIAA0825	ENST00000513200.7	c.1228-984A>G		intron_variant		5		A1
KIAA0825	ENST00000703867.1	c.1228-984A>G		intron_variant				P4

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39100 AN: 151926 Hom.: 6062 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.0360

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.258 AC: 39194 AN: 152044 Hom.: 6094 Cov.: 32 AF XY: 0.254 AC XY: 18874 AN XY: 74346

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.0361

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.258

Alfa AF: 0.209 Hom.: 7686

Bravo AF: 0.270

Asia WGS AF: 0.195 AC: 680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.6
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6869388; hg19: chr5-93810208; COSMIC: COSV56948196;