Variant rs16873582 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The ENST00000422774.2(KIAA1549):c.3036C>T(p.Ser1012=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.075 in 1,602,556 control chromosomes in the GnomAD database, including 4,849 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.084 ( 542 hom., cov: 33)

Exomes 𝑓: 0.074 ( 4307 hom. )

Consequence

KIAA1549
ENST00000422774.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.951

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 7-138911255-G-A is Benign according to our data. Variant chr7-138911255-G-A is described in ClinVar as [Benign]. Clinvar id is 1165056.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.951 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA1549	NM_001164665.2 linkuse as main transcript	c.3036C>T	p.Ser1012=	synonymous_variant	4/20	ENST00000422774.2	NP_001158137.1
KIAA1549	NM_020910.3 linkuse as main transcript	c.3036C>T	p.Ser1012=	synonymous_variant	4/20		NP_065961.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIAA1549	ENST00000422774.2 linkuse as main transcript	c.3036C>T	p.Ser1012=	synonymous_variant	4/20	1	NM_001164665.2	ENSP00000416040	A2	Q9HCM3-1
KIAA1549	ENST00000440172.5 linkuse as main transcript	c.3036C>T	p.Ser1012=	synonymous_variant	4/20	1		ENSP00000406661	P4	Q9HCM3-2

Frequencies

GnomAD3 genomes

AF:

0.0835

AC:

12709

AN:

152130

Hom.:

541

Cov.:

show subpopulations

Gnomad AFR

AF:

0.124

Gnomad AMI

AF:

0.0154

Gnomad AMR

AF:

0.0533

Gnomad ASJ

AF:

0.0851

Gnomad EAS

AF:

0.0572

Gnomad SAS

AF:

0.0712

Gnomad FIN

AF:

0.0438

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.0755

Gnomad OTH

AF:

0.0799

GnomAD3 exomes

AF:

0.0670

AC:

15638

AN:

233480

Hom.:

600

AF XY:

0.0674

AC XY:

8490

AN XY:

126018

show subpopulations

Gnomad AFR exome

AF:

0.128

Gnomad AMR exome

AF:

0.0343

Gnomad ASJ exome

AF:

0.0779

Gnomad EAS exome

AF:

0.0553

Gnomad SAS exome

AF:

0.0705

Gnomad FIN exome

AF:

0.0425

Gnomad NFE exome

AF:

0.0738

Gnomad OTH exome

AF:

0.0677

GnomAD4 exome

AF:

0.0741

AC:

107534

AN:

1450308

Hom.:

4307

Cov.:

AF XY:

0.0738

AC XY:

53140

AN XY:

720358

show subpopulations

Gnomad4 AFR exome

AF:

0.126

Gnomad4 AMR exome

AF:

0.0373

Gnomad4 ASJ exome

AF:

0.0754

Gnomad4 EAS exome

AF:

0.0576

Gnomad4 SAS exome

AF:

0.0711

Gnomad4 FIN exome

AF:

0.0445

Gnomad4 NFE exome

AF:

0.0761

Gnomad4 OTH exome

AF:

0.0755

GnomAD4 genome

AF:

0.0836

AC:

12721

AN:

152248

Hom.:

542

Cov.:

AF XY:

0.0818

AC XY:

6091

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.124

Gnomad4 AMR

AF:

0.0532

Gnomad4 ASJ

AF:

0.0851

Gnomad4 EAS

AF:

0.0571

Gnomad4 SAS

AF:

0.0714

Gnomad4 FIN

AF:

0.0438

Gnomad4 NFE

AF:

0.0755

Gnomad4 OTH

AF:

0.0829

Alfa

AF:

0.0760

Hom.:

756

Bravo

AF:

0.0845

Asia WGS

AF:

0.0590

AC:

208

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

Retinal dystrophy

Benign:1

Benign, criteria provided, single submitter

research

Dept Of Ophthalmology, Nagoya University

Oct 01, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

1.3

DANN

Benign

0.68

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over