12-88532513-CAAAA-CAAAAAA

Position:

• chr12-88532513-CAAAA-CAAAAAA

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS1

The NM_000899.5(KITLG):​c.130-12_130-11dupTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000772 in 1,305,048 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000043 (0 hom., cov: 30)
  • Exomes 𝑓: 0.00086 (0 hom.)
• Consequence: KITLG NM_000899.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318

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 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0000425 (6/141150) while in subpopulation AFR AF= 0.000157 (6/38306). AF 95% confidence interval is 0.0000681. There are 0 homozygotes in gnomad4. There are 3 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KITLG	NM_000899.5	c.130-12_130-11dupTT		intron_variant		ENST00000644744.1	NP_000890.1
KITLG	NM_003994.6	c.130-12_130-11dupTT		intron_variant			NP_003985.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KITLG	ENST00000644744.1	c.130-12_130-11dupTT		intron_variant			NM_000899.5	ENSP00000495951.1

Frequencies

GnomAD3 genomes AF: 0.0000425 AC: 6 AN: 141098 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.000157

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000741 AC: 88 AN: 118740 Hom.: 0 AF XY: 0.000852 AC XY: 54 AN XY: 63404

Gnomad AFR exome AF: 0.000477

Gnomad AMR exome AF: 0.00129

Gnomad ASJ exome AF: 0.000496

Gnomad EAS exome AF: 0.000142

Gnomad SAS exome AF: 0.00127

Gnomad FIN exome AF: 0.00111

Gnomad NFE exome AF: 0.000574

Gnomad OTH exome AF: 0.000375

GnomAD4 exome AF: 0.000861 AC: 1002 AN: 1163898 Hom.: 0 Cov.: 23 AF XY: 0.000854 AC XY: 493 AN XY: 577512

Gnomad4 AFR exome AF: 0.00106

Gnomad4 AMR exome AF: 0.000592

Gnomad4 ASJ exome AF: 0.000360

Gnomad4 EAS exome AF: 0.000137

Gnomad4 SAS exome AF: 0.00100

Gnomad4 FIN exome AF: 0.000511

Gnomad4 NFE exome AF: 0.000911

Gnomad4 OTH exome AF: 0.000785

GnomAD4 genome AF: 0.0000425 AC: 6 AN: 141150 Hom.: 0 Cov.: 30 AF XY: 0.0000439 AC XY: 3 AN XY: 68410

Gnomad4 AFR AF: 0.000157

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11428619; hg19: chr12-88926290;