Variant 12-88532513-CAAAA-CAAAAA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_000899.5(KITLG):c.130-11dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 1,239,402 control chromosomes in the GnomAD database, including 2,098 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.094 ( 601 hom., cov: 30)

Exomes 𝑓: 0.14 ( 1497 hom. )

Consequence

KITLG
NM_000899.5 intron

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.318

Variant links:

Genes affected

KITLG (HGNC:6343): (KIT ligand) This gene encodes the ligand of the tyrosine-kinase receptor encoded by the KIT locus. This ligand is a pleiotropic factor that acts in utero in germ cell and neural cell development, and hematopoiesis, all believed to reflect a role in cell migration. In adults, it functions pleiotropically, while mostly noted for its continued requirement in hematopoiesis. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

KITLG links:

KITLG (HGNC:):

KITLG links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 12-88532513-C-CA is Benign according to our data. Variant chr12-88532513-C-CA is described in ClinVar as [Likely_benign]. Clinvar id is 517646.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KITLG	NM_000899.5 linkuse as main transcript	c.130-11dupT		intron_variant		ENST00000644744.1	NP_000890.1	P21583-1A0A024RBC0
KITLG	NM_003994.6 linkuse as main transcript	c.130-11dupT		intron_variant			NP_003985.2	P21583-2A0A024RBF5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KITLG	ENST00000644744.1 linkuse as main transcript	c.130-11dupT		intron_variant			NM_000899.5	ENSP00000495951.1		P21583-1

Frequencies

GnomAD3 genomes

AF:

0.0944

AC:

13312

AN:

141008

Hom.:

600

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0837

Gnomad AMI

AF:

0.0752

Gnomad AMR

AF:

0.0835

Gnomad ASJ

AF:

0.0663

Gnomad EAS

AF:

0.0115

Gnomad SAS

AF:

0.103

Gnomad FIN

AF:

0.0974

Gnomad MID

AF:

0.0690

Gnomad NFE

AF:

0.110

Gnomad OTH

AF:

0.110

GnomAD3 exomes

AF:

0.165

AC:

19607

AN:

118740

Hom.:

178

AF XY:

0.172

AC XY:

10933

AN XY:

63404

show subpopulations

Gnomad AFR exome

AF:

0.132

Gnomad AMR exome

AF:

0.145

Gnomad ASJ exome

AF:

0.158

Gnomad EAS exome

AF:

0.0296

Gnomad SAS exome

AF:

0.211

Gnomad FIN exome

AF:

0.160

Gnomad NFE exome

AF:

0.181

Gnomad OTH exome

AF:

0.181

GnomAD4 exome

AF:

0.136

AC:

148939

AN:

1098342

Hom.:

1497

Cov.:

AF XY:

0.137

AC XY:

74407

AN XY:

543938

show subpopulations

Gnomad4 AFR exome

AF:

0.110

Gnomad4 AMR exome

AF:

0.0931

Gnomad4 ASJ exome

AF:

0.104

Gnomad4 EAS exome

AF:

0.0545

Gnomad4 SAS exome

AF:

0.143

Gnomad4 FIN exome

AF:

0.116

Gnomad4 NFE exome

AF:

0.142

Gnomad4 OTH exome

AF:

0.132

GnomAD4 genome

AF:

0.0944

AC:

13315

AN:

141060

Hom.:

601

Cov.:

AF XY:

0.0929

AC XY:

6353

AN XY:

68370

show subpopulations

Gnomad4 AFR

AF:

0.0838

Gnomad4 AMR

AF:

0.0834

Gnomad4 ASJ

AF:

0.0663

Gnomad4 EAS

AF:

0.0116

Gnomad4 SAS

AF:

0.103

Gnomad4 FIN

AF:

0.0974

Gnomad4 NFE

AF:

0.110

Gnomad4 OTH

AF:

0.108

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 18, 2019	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Nov 13, 2017

This variant is present in 15% (21777/141927) of all chromosomes in the Genome A ggregation Database (gnomAD, http://gnomad.broadinstitute.org, rs11428619) and i s therefore benign. -

Hyperpigmentation with or without hypopigmentation, familial progressive;C2674081:SKIN/HAIR/EYE PIGMENTATION 7, DARK/LIGHT SKIN;C4225241:Autosomal dominant nonsyndromic hearing loss 69

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Sep 27, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

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