chr5-94474503-T-C

Variant names:

• chr5-94474503-T-C
• rs6869388
• NM_001145678.3:c.1228-984A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

Genes affected

KIAA0825 (HGNC:28532): (KIAA0825)

KIAA0825 Gene-Disease associations (from GenCC):

• polydactyly, postaxial, type a10

  Inheritance: AR Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
• postaxial polydactyly type A

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000309437 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001145678.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA0825	NM_001145678.3	MANE Select	c.1228-984A>G		intron	N/A	NP_001139150.1
	KIAA0825	NM_001385712.1		c.1228-984A>G		intron	N/A	NP_001372641.1
	KIAA0825	NM_001388325.1		c.1228-984A>G		intron	N/A	NP_001375254.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA0825	ENST00000682413.1	MANE Select	c.1228-984A>G		intron	N/A	ENSP00000506760.1
	KIAA0825	ENST00000504117.1	TSL:1	n.75-984A>G		intron	N/A
	KIAA0825	ENST00000703867.1		c.1228-984A>G		intron	N/A	ENSP00000515512.1

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

African (AFR) AF: 0.434 AC: 17988 AN: 41422

American (AMR) AF: 0.198 AC: 3029 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 818 AN: 3466

East Asian (EAS) AF: 0.0361 AC: 187 AN: 5178

South Asian (SAS) AF: 0.249 AC: 1200 AN: 4822

European-Finnish (FIN) AF: 0.179 AC: 1891 AN: 10562

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13130 AN: 67996

Other (OTH) AF: 0.258 AC: 544 AN: 2106

Alfa AF: 0.214 Hom.: 16887

Bravo AF: 0.270

Asia WGS AF: 0.195 AC: 680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.49
PhyloP100		0.013
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6869388; hg19: chr5-93810208;