chr11-47395561-C-CG

Position:

• chr11-47395561-C-CG

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The ENST00000666926.1(SLC39A13-AS1):​n.336_337insC variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00896 in 152,588 control chromosomes in the GnomAD database, including 17 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0090 (17 hom., cov: 32)
  • Exomes 𝑓: 0.011 (0 hom.)
• Consequence: SLC39A13-AS1 ENST00000666926.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.122

Genes affected

SLC39A13-AS1 (HGNC:56351): (SLC39A13 antisense RNA 1)

SPI1 (HGNC:11241): (Spi-1 proto-oncogene) This gene encodes an ETS-domain transcription factor that activates gene expression during myeloid and B-lymphoid cell development. The nuclear protein binds to a purine-rich sequence known as the PU-box found near the promoters of target genes, and regulates their expression in coordination with other transcription factors and cofactors. The protein can also regulate alternative splicing of target genes. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 11-47395561-C-CG is Benign according to our data. Variant chr11-47395561-C-CG is described in ClinVar as [Benign]. Clinvar id is 3250508.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 17 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC39A13-AS1	NR_182305.1	n.332-11730_332-11729insC		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC39A13-AS1	ENST00000666926.1	n.336_337insC		non_coding_transcript_exon_variant	2/3

Frequencies

GnomAD3 genomes AF: 0.00895 AC: 1362 AN: 152192 Hom.: 17 Cov.: 32

Gnomad AFR AF: 0.00207

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0139

Gnomad ASJ AF: 0.0305

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00228

Gnomad FIN AF: 0.00565

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0124

Gnomad OTH AF: 0.0148

GnomAD4 exome AF: 0.0108 AC: 3 AN: 278 Hom.: 0 Cov.: 0 AF XY: 0.00495 AC XY: 1 AN XY: 202

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0149

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00896 AC: 1364 AN: 152310 Hom.: 17 Cov.: 32 AF XY: 0.00878 AC XY: 654 AN XY: 74472

Gnomad4 AFR AF: 0.00207

Gnomad4 AMR AF: 0.0139

Gnomad4 ASJ AF: 0.0305

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00248

Gnomad4 FIN AF: 0.00565

Gnomad4 NFE AF: 0.0125

Gnomad4 OTH AF: 0.0147

Alfa AF: 0.0101 Hom.: 2

Bravo AF: 0.00971

Asia WGS AF: 0.00144 AC: 5 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Aug 01, 2024

SLC39A13-AS1: BS1, BS2 -

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: rs565330072; hg19: chr11-47417112;