dbSNP rs896193: KIAA1549:c.*4595G>A (chr7-138833311-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001164665.2(KIAA1549):c.*4595G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.782 in 232,280 control chromosomes in the GnomAD database, including 72,311 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 0.79 ( 48117 hom., cov: 33)

Exomes 𝑓: 0.77 ( 24194 hom. )

Consequence

KIAA1549
NM_001164665.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.914

Publications

3 publications found

Variant links:

Genes affected

KIAA1549 (HGNC:22219): (KIAA1549) The protein encoded by this gene belongs to the UPF0606 family. This gene has been found to be fused to the BRAF oncogene in many cases of pilocytic astrocytoma. The fusion results from 2Mb tandem duplications at 7q34. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2012]

KIAA1549 links:

TMEM213 (HGNC:27220): (transmembrane protein 213) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TMEM213 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA1549	NM_001164665.2 link	c.*4595G>A		3_prime_UTR_variant	Exon 20 of 20	ENST00000422774.2	NP_001158137.1	Q9HCM3-1
KIAA1549	NM_020910.3 link	c.*4595G>A		3_prime_UTR_variant	Exon 20 of 20		NP_065961.2	Q9HCM3-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
KIAA1549	ENST00000422774.2 link	c.*4595G>A	3_prime_UTR_variant	Exon 20 of 20	1	NM_001164665.2	ENSP00000416040.2	Q9HCM3-1
KIAA1549	ENST00000440172.5 link	c.*4595G>A	3_prime_UTR_variant	Exon 20 of 20	1		ENSP00000406661.1	Q9HCM3-2
TMEM213	ENST00000413208.1 link	c.155-4558C>T	intron_variant	Intron 2 of 2	3		ENSP00000401570.1	A2RRL7-4

Frequencies

GnomAD3 genomes

AF:

0.787

AC:

119629

AN:

152064

Hom.:

48051

Cov.:

show subpopulations

Gnomad AFR

AF:

0.950

Gnomad AMI

AF:

0.753

Gnomad AMR

AF:

0.713

Gnomad ASJ

AF:

0.771

Gnomad EAS

AF:

0.913

Gnomad SAS

AF:

0.686

Gnomad FIN

AF:

0.660

Gnomad MID

AF:

0.804

Gnomad NFE

AF:

0.722

Gnomad OTH

AF:

0.797

GnomAD4 exome

AF:

0.773

AC:

61899

AN:

80098

Hom.:

24194

Cov.:

AF XY:

0.772

AC XY:

28481

AN XY:

36878

show subpopulations

African (AFR)

AF:

0.953

AC:

3670

AN:

3852

American (AMR)

AF:

0.712

AC:

1759

AN:

2470

Ashkenazi Jewish (ASJ)

AF:

0.773

AC:

3927

AN:

5078

East Asian (EAS)

AF:

0.954

AC:

10768

AN:

11286

South Asian (SAS)

AF:

0.669

AC:

463

AN:

692

European-Finnish (FIN)

AF:

0.700

AC:

AN:

Middle Eastern (MID)

AF:

0.808

AC:

396

AN:

490

European-Non Finnish (NFE)

AF:

0.723

AC:

35780

AN:

49496

Other (OTH)

AF:

0.763

AC:

5094

AN:

6674

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

674

1349

2023

2698

3372

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

140

280

420

560

700

<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:

0.787

AC:

119756

AN:

152182

Hom.:

48117

Cov.:

AF XY:

0.782

AC XY:

58155

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.950

AC:

39473

AN:

41538

American (AMR)

AF:

0.713

AC:

10898

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.771

AC:

2677

AN:

3472

East Asian (EAS)

AF:

0.912

AC:

4732

AN:

5186

South Asian (SAS)

AF:

0.687

AC:

3310

AN:

4816

European-Finnish (FIN)

AF:

0.660

AC:

6978

AN:

10576

Middle Eastern (MID)

AF:

0.806

AC:

237

AN:

294

European-Non Finnish (NFE)

AF:

0.722

AC:

49079

AN:

67992

Other (OTH)

AF:

0.799

AC:

1687

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1238

2476

3713

4951

6189

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

858

1716

2574

3432

4290

<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:

0.741

Hom.:

69826

Bravo

AF:

0.805

Asia WGS

AF:

0.826

AC:

2872

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

4.3

(source)

DANN

Benign

0.71

PhyloP100

0.91

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