rs1472899

chr12-88557708-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000899.5(KITLG):c.16-11843G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 151,930 control chromosomes in the GnomAD database, including 36,439 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 0.66 (36439 hom., cov: 31)
• Consequence: KITLG NM_000899.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KITLG	NM_000899.5	c.16-11843G>A		intron_variant		ENST00000644744.1
KITLG	NM_003994.6	c.16-11843G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KITLG	ENST00000644744.1	c.16-11843G>A		intron_variant			NM_000899.5	P1

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99536 AN: 151812 Hom.: 36435 Cov.: 31

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.752

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.696

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.655 AC: 99559 AN: 151930 Hom.: 36439 Cov.: 31 AF XY: 0.660 AC XY: 49072 AN XY: 74298

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.780

Gnomad4 ASJ AF: 0.856

Gnomad4 EAS AF: 0.722

Gnomad4 SAS AF: 0.797

Gnomad4 FIN AF: 0.783

Gnomad4 NFE AF: 0.798

Gnomad4 OTH AF: 0.697

Alfa AF: 0.762 Hom.: 16344

Bravo AF: 0.636

Asia WGS AF: 0.721 AC: 2507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.5
Dann	Benign	0.61

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

Other links and lift over

dbSNP: rs1472899; hg19: chr12-88951485;