dbSNP rs7770041: KIAA0319:c.*42A>G (chr6-24547123-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014809.4(KIAA0319):c.*42A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0241 in 1,603,148 control chromosomes in the GnomAD database, including 868 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 0.041 ( 267 hom., cov: 33)

Exomes 𝑓: 0.022 ( 601 hom. )

Consequence

KIAA0319
NM_014809.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.618

Publications

4 publications found

Variant links:

Genes affected

KIAA0319 (HGNC:21580): (KIAA0319) This gene encodes a transmembrane protein that contains a large extracellular domain with multiple polycystic kidney disease (PKD) domains. The encoded protein may play a role in the development of the cerebral cortex by regulating neuronal migration and cell adhesion. Single nucleotide polymorphisms in this gene are associated with dyslexia. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2011]

KIAA0319 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA0319	NM_014809.4 link	c.*42A>G		3_prime_UTR_variant	Exon 21 of 21	ENST00000378214.8	NP_055624.2	Q5VV43-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA0319	ENST00000378214.8 link	c.*42A>G		3_prime_UTR_variant	Exon 21 of 21	1	NM_014809.4	ENSP00000367459.3		Q5VV43-1

Frequencies

GnomAD3 genomes

AF:

0.0409

AC:

6224

AN:

152200

Hom.:

264

Cov.:

show subpopulations

Gnomad AFR

AF:

0.107

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0182

Gnomad ASJ

AF:

0.00259

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.00207

Gnomad FIN

AF:

0.00320

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0205

Gnomad OTH

AF:

0.0320

GnomAD2 exomes

AF:

0.0186

AC:

4647

AN:

249378

AF XY:

0.0163

show subpopulations

Gnomad AFR exome

AF:

0.111

Gnomad AMR exome

AF:

0.0109

Gnomad ASJ exome

AF:

0.00172

Gnomad EAS exome

AF:

0.000870

Gnomad FIN exome

AF:

0.00337

Gnomad NFE exome

AF:

0.0198

Gnomad OTH exome

AF:

0.0131

GnomAD4 exome

AF:

0.0224

AC:

32453

AN:

1450830

Hom.:

601

Cov.:

AF XY:

0.0213

AC XY:

15417

AN XY:

722122

show subpopulations

African (AFR)

AF:

0.113

AC:

3759

AN:

33218

American (AMR)

AF:

0.0117

AC:

521

AN:

44606

Ashkenazi Jewish (ASJ)

AF:

0.00174

AC:

AN:

25894

East Asian (EAS)

AF:

0.000505

AC:

AN:

39628

South Asian (SAS)

AF:

0.00203

AC:

174

AN:

85584

European-Finnish (FIN)

AF:

0.00345

AC:

183

AN:

53098

Middle Eastern (MID)

AF:

0.0185

AC:

106

AN:

5738

European-Non Finnish (NFE)

AF:

0.0238

AC:

26220

AN:

1103038

Other (OTH)

AF:

0.0237

AC:

1425

AN:

60026

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1537

3074

4610

6147

7684

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1102

2204

3306

4408

5510

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0409

AC:

6234

AN:

152318

Hom.:

267

Cov.:

AF XY:

0.0381

AC XY:

2835

AN XY:

74476

show subpopulations

African (AFR)

AF:

0.107

AC:

4428

AN:

41556

American (AMR)

AF:

0.0182

AC:

278

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.00259

AC:

AN:

3472

East Asian (EAS)

AF:

0.000386

AC:

AN:

5184

South Asian (SAS)

AF:

0.00207

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00320

AC:

AN:

10618

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0205

AC:

1396

AN:

68036

Other (OTH)

AF:

0.0317

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

285

571

856

1142

1427

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

180

240

300

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0269

Hom.:

150

Bravo

AF:

0.0454

Asia WGS

AF:

0.00635

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

3.9

(source)

DANN

Benign

0.86

PhyloP100

-0.62

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over