Variant 11-47395561-C-CG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The ENST00000527426.1(SLC39A13-AS1):n.79dupC 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
ENST00000527426.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.122

Variant links:

Genes affected

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

SLC39A13-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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	Effect	Exon rank
SLC39A13-AS1	NR_182304.1 link	n.347dupC	non_coding_transcript_exon_variant	Exon 2 of 3
SLC39A13-AS1	NR_182306.1 link	n.437dupC	non_coding_transcript_exon_variant	Exon 3 of 4
SLC39A13-AS1	NR_182308.1 link	n.385dupC	non_coding_transcript_exon_variant	Exon 3 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SLC39A13-AS1	ENST00000527426.1 link	n.79dupC	non_coding_transcript_exon_variant	Exon 1 of 2	3
SLC39A13-AS1	ENST00000532943.5 link	n.195dupC	non_coding_transcript_exon_variant	Exon 3 of 4	3
SLC39A13-AS1	ENST00000659838.2 link	n.46dupC	non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.00895

AC:

1362

AN:

152192

Hom.:

Cov.:

show subpopulations

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:

AN:

278

Hom.:

Cov.:

AF XY:

0.00495

AC XY:

AN XY:

202

show subpopulations

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.:

Cov.:

AF XY:

0.00878

AC XY:

654

AN XY:

74472

show subpopulations

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.:

Bravo

AF:

0.00971

Asia WGS

AF:

0.00144

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Dec 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

SLC39A13-AS1: BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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