rs13154972

Variant names:

• chr5-94363527-T-C
• rs13154972
• NM_001145678.3:c.3710+20841A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-94363527-T-C
• chr5-94363527-T-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.3710+20841A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 152,082 control chromosomes in the GnomAD database, including 5,109 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 0.21 (5109 hom., cov: 31)
• Consequence: KIAA0825 NM_001145678.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.328
• Publications: 5 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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA0825	NM_001145678.3	c.3710+20841A>G		intron_variant	Intron 20 of 20	ENST00000682413.1	NP_001139150.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA0825	ENST00000682413.1	c.3710+20841A>G		intron_variant	Intron 20 of 20		NM_001145678.3	ENSP00000506760.1
KIAA0825	ENST00000703867.1	c.3725+20841A>G		intron_variant	Intron 20 of 20			ENSP00000515512.1
KIAA0825	ENST00000513200.7	c.3710+20841A>G		intron_variant	Intron 19 of 19	5		ENSP00000424618.2

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32583 AN: 151964 Hom.: 5095 Cov.: 31

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.0980

Gnomad SAS AF: 0.0979

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.215 AC: 32643 AN: 152082 Hom.: 5109 Cov.: 31 AF XY: 0.210 AC XY: 15632 AN XY: 74364

African (AFR) AF: 0.450 AC: 18636 AN: 41422

American (AMR) AF: 0.117 AC: 1788 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 430 AN: 3470

East Asian (EAS) AF: 0.0979 AC: 507 AN: 5180

South Asian (SAS) AF: 0.0982 AC: 473 AN: 4818

European-Finnish (FIN) AF: 0.135 AC: 1428 AN: 10596

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8862 AN: 67996

Other (OTH) AF: 0.193 AC: 407 AN: 2110

Alfa AF: 0.146 Hom.: 4095

Bravo AF: 0.225

Asia WGS AF: 0.162 AC: 565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.28
DANN	Benign	0.65
PhyloP100		-0.33
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: rs13154972; hg19: chr5-93699232;