Genetic Variant NM_019590.5:c.1155A>G (chr10-24473536-A-G) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_019590.5(KIAA1217):c.1155A>G(p.Ala385Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 1,614,008 control chromosomes in the GnomAD database, including 10,875 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 0.093 ( 937 hom., cov: 32)

Exomes 𝑓: 0.11 ( 9938 hom. )

Consequence

KIAA1217
NM_019590.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.79

Publications

8 publications found

Variant links:

Genes affected

KIAA1217 (HGNC:25428): (KIAA1217) Predicted to be involved in embryonic skeletal system development. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

KIAA1217 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP7

Synonymous conserved (PhyloP=-4.79 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA1217	NM_019590.5 link	c.1155A>G	p.Ala385Ala	synonymous_variant	Exon 6 of 21	ENST00000376454.8	NP_062536.2	Q5T5P2-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA1217	ENST00000376454.8 link	c.1155A>G	p.Ala385Ala	synonymous_variant	Exon 6 of 21	1	NM_019590.5	ENSP00000365637.3		Q5T5P2-1

Frequencies

GnomAD3 genomes

AF:

0.0926

AC:

14076

AN:

152048

Hom.:

930

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0203

Gnomad AMI

AF:

0.166

Gnomad AMR

AF:

0.107

Gnomad ASJ

AF:

0.0551

Gnomad EAS

AF:

0.155

Gnomad SAS

AF:

0.0367

Gnomad FIN

AF:

0.258

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.109

Gnomad OTH

AF:

0.0790

GnomAD2 exomes

AF:

0.109

AC:

27359

AN:

251174

AF XY:

0.106

show subpopulations

Gnomad AFR exome

AF:

0.0177

Gnomad AMR exome

AF:

0.104

Gnomad ASJ exome

AF:

0.0593

Gnomad EAS exome

AF:

0.161

Gnomad FIN exome

AF:

0.258

Gnomad NFE exome

AF:

0.111

Gnomad OTH exome

AF:

0.102

GnomAD4 exome

AF:

0.109

AC:

159350

AN:

1461842

Hom.:

9938

Cov.:

AF XY:

0.107

AC XY:

77570

AN XY:

727216

show subpopulations

African (AFR)

AF:

0.0161

AC:

540

AN:

33478

American (AMR)

AF:

0.107

AC:

4765

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.0583

AC:

1524

AN:

26134

East Asian (EAS)

AF:

0.150

AC:

5963

AN:

39698

South Asian (SAS)

AF:

0.0364

AC:

3143

AN:

86252

European-Finnish (FIN)

AF:

0.252

AC:

13484

AN:

53414

Middle Eastern (MID)

AF:

0.0224

AC:

129

AN:

5768

European-Non Finnish (NFE)

AF:

0.112

AC:

124034

AN:

1111980

Other (OTH)

AF:

0.0955

AC:

5768

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

9175

18350

27524

36699

45874

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4474

8948

13422

17896

22370

<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:

0.0926

AC:

14090

AN:

152166

Hom.:

937

Cov.:

AF XY:

0.0993

AC XY:

7383

AN XY:

74380

show subpopulations

African (AFR)

AF:

0.0202

AC:

839

AN:

41544

American (AMR)

AF:

0.108

AC:

1655

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0551

AC:

191

AN:

3468

East Asian (EAS)

AF:

0.156

AC:

804

AN:

5162

South Asian (SAS)

AF:

0.0361

AC:

174

AN:

4822

European-Finnish (FIN)

AF:

0.258

AC:

2729

AN:

10564

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.109

AC:

7379

AN:

67992

Other (OTH)

AF:

0.0782

AC:

165

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

619

1238

1857

2476

3095

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

160

320

480

640

800

<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:

0.0944

Hom.:

410

Bravo

AF:

0.0803

Asia WGS

AF:

0.0840

AC:

291

AN:

3478

EpiCase

AF:

0.0935

EpiControl

AF:

0.0922

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.044

(source)

DANN

Benign

0.40

PhyloP100

-4.8

Mutation Taster

=99/1

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