NM_001145678.3:c.1872+1849A>G

Variant names:

• chr5-94468112-T-C
• rs10514384
• NM_001145678.3:c.1872+1849A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001145678.3(KIAA0825):​c.1872+1849A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,220 control chromosomes in the GnomAD database, including 1,879 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 0.14 (1879 hom., cov: 32)
• Consequence: KIAA0825 NM_001145678.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440
• Publications: 3 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA0825	NM_001145678.3	c.1872+1849A>G		intron_variant	Intron 10 of 20	ENST00000682413.1	NP_001139150.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA0825	ENST00000682413.1	c.1872+1849A>G		intron_variant	Intron 10 of 20		NM_001145678.3	ENSP00000506760.1

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21756 AN: 152102 Hom.: 1880 Cov.: 32

Gnomad AFR AF: 0.0574

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.143 AC: 21746 AN: 152220 Hom.: 1879 Cov.: 32 AF XY: 0.144 AC XY: 10705 AN XY: 74414

African (AFR) AF: 0.0574 AC: 2385 AN: 41558

American (AMR) AF: 0.117 AC: 1793 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 520 AN: 3472

East Asian (EAS) AF: 0.103 AC: 535 AN: 5180

South Asian (SAS) AF: 0.170 AC: 818 AN: 4822

European-Finnish (FIN) AF: 0.240 AC: 2544 AN: 10582

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12739 AN: 67992

Other (OTH) AF: 0.140 AC: 296 AN: 2114

Alfa AF: 0.170 Hom.: 1993

Bravo AF: 0.130

Asia WGS AF: 0.122 AC: 427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	16
DANN	Benign	0.73
PhyloP100		-0.044
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: rs10514384; hg19: chr5-93803817;