5-94462460-T-C

Variant names:

• chr5-94462460-T-C
• NM_001145678.3:c.2173A>G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001145678.3(KIAA0825):​c.2173A>G​(p.Lys725Glu) variant causes a missense change. The variant allele was found at a frequency of 0.0000123 in 1,379,340 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.000012 (0 hom.)
• Consequence: KIAA0825 NM_001145678.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.81

Genes affected

KIAA0825 (HGNC:28532): (KIAA0825)

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.26079434).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA0825	NM_001145678.3	c.2173A>G	p.Lys725Glu	missense_variant	Exon 12 of 21	ENST00000682413.1	NP_001139150.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA0825	ENST00000682413.1	c.2173A>G	p.Lys725Glu	missense_variant	Exon 12 of 21		NM_001145678.3	ENSP00000506760.1
KIAA0825	ENST00000504117.1	n.1020A>G		non_coding_transcript_exon_variant	Exon 6 of 9	1
KIAA0825	ENST00000703867.1	c.2173A>G	p.Lys725Glu	missense_variant	Exon 12 of 21			ENSP00000515512.1
KIAA0825	ENST00000513200.7	c.2173A>G	p.Lys725Glu	missense_variant	Exon 11 of 20	5		ENSP00000424618.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.0000123 AC: 17 AN: 1379340 Hom.: 0 Cov.: 26 AF XY: 0.0000117 AC XY: 8 AN XY: 681252

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000160

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Uncertain	0.054	T
BayesDel_noAF	Benign	-0.16
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.047	T
Eigen	Uncertain	0.47
Eigen_PC	Uncertain	0.49
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Benign	0.77	T
M_CAP	Benign	0.021	T
MetaRNN	Benign	0.26	T
MetaSVM	Benign	-0.56	T
MutationAssessor	Uncertain	2.6	M
PrimateAI	Uncertain	0.52	T
PROVEAN	Benign	-0.84	N
REVEL	Benign	0.11
Sift	Benign	0.033	D
Sift4G	Uncertain	0.033	D
Polyphen		0.91	P
Vest4		0.34
MutPred		0.45		Loss of methylation at K725 (P = 0.001);
MVP		0.29
ClinPred		0.83	D
GERP RS		5.5
Varity_R		0.29

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr5-93798165;