5-94417169-C-T

Position:

• chr5-94417169-C-T

Variant summary

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

The NM_001145678.3(KIAA0825):​c.2662+32G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 1,532,666 control chromosomes in the GnomAD database, including 11,594 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 0.12 (1191 hom., cov: 33)
  • Exomes 𝑓: 0.12 (10403 hom.)
• Consequence: KIAA0825 NM_001145678.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA0825	NM_001145678.3	c.2662+32G>A		intron_variant		ENST00000682413.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA0825	ENST00000682413.1	c.2662+32G>A		intron_variant			NM_001145678.3	A1
KIAA0825	ENST00000504117.1	n.1556G>A		non_coding_transcript_exon_variant	9/9	1
KIAA0825	ENST00000513200.7	c.2662+32G>A		intron_variant		5		A1
KIAA0825	ENST00000703867.1	c.2677+32G>A		intron_variant				P4

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17753 AN: 151946 Hom.: 1189 Cov.: 33

Gnomad AFR AF: 0.0833

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.0841

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.114

GnomAD3 exomes AF: 0.132 AC: 20485 AN: 154804 Hom.: 1587 AF XY: 0.132 AC XY: 10799 AN XY: 82100

Gnomad AFR exome AF: 0.0845

Gnomad AMR exome AF: 0.156

Gnomad ASJ exome AF: 0.0786

Gnomad EAS exome AF: 0.240

Gnomad SAS exome AF: 0.122

Gnomad FIN exome AF: 0.168

Gnomad NFE exome AF: 0.112

Gnomad OTH exome AF: 0.119

GnomAD4 exome AF: 0.117 AC: 161203 AN: 1380604 Hom.: 10403 Cov.: 26 AF XY: 0.117 AC XY: 79926 AN XY: 681974

Gnomad4 AFR exome AF: 0.0796

Gnomad4 AMR exome AF: 0.150

Gnomad4 ASJ exome AF: 0.0784

Gnomad4 EAS exome AF: 0.275

Gnomad4 SAS exome AF: 0.119

Gnomad4 FIN exome AF: 0.163

Gnomad4 NFE exome AF: 0.110

Gnomad4 OTH exome AF: 0.118

GnomAD4 genome AF: 0.117 AC: 17767 AN: 152062 Hom.: 1191 Cov.: 33 AF XY: 0.120 AC XY: 8898 AN XY: 74306

Gnomad4 AFR AF: 0.0831

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.0841

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.118

Alfa AF: 0.113 Hom.: 568

Bravo AF: 0.112

Asia WGS AF: 0.187 AC: 649 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	3.9
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs29911; hg19: chr5-93752874; COSMIC: COSV56952765;