rs17376456

chr5-94221997-A-G

Variant summary

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

The NM_001145678.3(KIAA0825):c.3711-67873T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0874 in 152,136 control chromosomes in the GnomAD database, including 733 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 0.087 (733 hom., cov: 32)
• Consequence: KIAA0825 NM_001145678.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470

Genes affected

KIAA0825 (HGNC:28532): (KIAA0825)

LOC105379087 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA0825	NM_001145678.3	c.3711-67873T>C		intron_variant		ENST00000682413.1
LOC105379087	XR_001742443.2	n.391+4536A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA0825	ENST00000682413.1	c.3711-67873T>C		intron_variant			NM_001145678.3	A1
KIAA0825	ENST00000513200.7	c.3711-67873T>C		intron_variant		5		A1
KIAA0825	ENST00000703867.1	c.3726-67873T>C		intron_variant				P4

Frequencies

GnomAD3 genomes AF: 0.0874 AC: 13290 AN: 152018 Hom.: 734 Cov.: 32

Gnomad AFR AF: 0.0459

Gnomad AMI AF: 0.0670

Gnomad AMR AF: 0.0767

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.0457

Gnomad SAS AF: 0.0707

Gnomad FIN AF: 0.0289

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0874 AC: 13291 AN: 152136 Hom.: 733 Cov.: 32 AF XY: 0.0834 AC XY: 6206 AN XY: 74378

Gnomad4 AFR AF: 0.0458

Gnomad4 AMR AF: 0.0766

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.0456

Gnomad4 SAS AF: 0.0710

Gnomad4 FIN AF: 0.0289

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.109

Alfa AF: 0.119 Hom.: 1747

Bravo AF: 0.0890

Asia WGS AF: 0.0700 AC: 244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.2
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17376456; hg19: chr5-93557702; COSMIC: COSV70247317;