rs29911

Variant names:

• chr5-94417169-C-T
• rs29911
• ENST00000504117.1:n.1556G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000504117.1(KIAA0825):​n.1556G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 1,532,666 control chromosomes in the GnomAD database, including 11,594 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 0.12 (1191 hom., cov: 33)
  • Exomes 𝑓: 0.12 (10403 hom.)
• Consequence: KIAA0825 ENST00000504117.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• Publications: 6 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 (REVEL=0.004).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA0825	NM_001145678.3	c.2662+32G>A		intron_variant	Intron 15 of 20	ENST00000682413.1	NP_001139150.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA0825	ENST00000504117.1	n.1556G>A		non_coding_transcript_exon_variant	Exon 9 of 9	1
KIAA0825	ENST00000682413.1	c.2662+32G>A		intron_variant	Intron 15 of 20		NM_001145678.3	ENSP00000506760.1
KIAA0825	ENST00000703867.1	c.2677+32G>A		intron_variant	Intron 15 of 20			ENSP00000515512.1
KIAA0825	ENST00000513200.7	c.2662+32G>A		intron_variant	Intron 14 of 19	5		ENSP00000424618.2

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17753 AN: 151946 Hom.: 1189 Cov.: 33

Gnomad AFR AF: 0.0833

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.0841

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.114

GnomAD2 exomes AF: 0.132 AC: 20485 AN: 154804 AF XY: 0.132

Gnomad AFR exome AF: 0.0845

Gnomad AMR exome AF: 0.156

Gnomad ASJ exome AF: 0.0786

Gnomad EAS exome AF: 0.240

Gnomad FIN exome AF: 0.168

Gnomad NFE exome AF: 0.112

Gnomad OTH exome AF: 0.119

GnomAD4 exome AF: 0.117 AC: 161203 AN: 1380604 Hom.: 10403 Cov.: 26 AF XY: 0.117 AC XY: 79926 AN XY: 681974

African (AFR) AF: 0.0796 AC: 2486 AN: 31242

American (AMR) AF: 0.150 AC: 5365 AN: 35652

Ashkenazi Jewish (ASJ) AF: 0.0784 AC: 1962 AN: 25040

East Asian (EAS) AF: 0.275 AC: 9783 AN: 35512

South Asian (SAS) AF: 0.119 AC: 9339 AN: 78798

European-Finnish (FIN) AF: 0.163 AC: 7825 AN: 48050

Middle Eastern (MID) AF: 0.103 AC: 583 AN: 5650

European-Non Finnish (NFE) AF: 0.110 AC: 117092 AN: 1063304

Other (OTH) AF: 0.118 AC: 6768 AN: 57356

GnomAD4 genome AF: 0.117 AC: 17767 AN: 152062 Hom.: 1191 Cov.: 33 AF XY: 0.120 AC XY: 8898 AN XY: 74306

African (AFR) AF: 0.0831 AC: 3452 AN: 41526

American (AMR) AF: 0.145 AC: 2210 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0841 AC: 291 AN: 3462

East Asian (EAS) AF: 0.264 AC: 1363 AN: 5164

South Asian (SAS) AF: 0.129 AC: 622 AN: 4826

European-Finnish (FIN) AF: 0.167 AC: 1770 AN: 10572

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7695 AN: 67918

Other (OTH) AF: 0.118 AC: 248 AN: 2110

Alfa AF: 0.116 Hom.: 1910

Bravo AF: 0.112

Asia WGS AF: 0.187 AC: 649 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.9
DANN	Benign	0.48
PhyloP100		0.060
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: rs29911; hg19: chr5-93752874; COSMIC: COSV56952765;