chr11-47408641-T-TCGC

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001128225.3(SLC39A13):​c.-14_-12dupCGC variant causes a splice region change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.30 ( 6896 hom., cov: 0)
Exomes 𝑓: 0.41 ( 110 hom. )

Consequence

SLC39A13
NM_001128225.3 splice_region

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: 0.167
Variant links:
Genes affected
SLC39A13 (HGNC:20859): (solute carrier family 39 member 13) This gene encodes a member of the LIV-1 subfamily of the ZIP transporter family. The encoded transmembrane protein functions as a zinc transporter. Mutations in this gene have been associated with the spondylocheiro dysplastic form of Ehlers-Danlos syndrome. Alternate transcript variants have been found for this gene. [provided by RefSeq, Jan 2016]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 11-47408641-T-TCGC is Benign according to our data. Variant chr11-47408641-T-TCGC is described in ClinVar as [Benign]. Clinvar id is 517012.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLC39A13NM_001128225.3 linkuse as main transcriptc.-14_-12dupCGC splice_region_variant 1/10 ENST00000362021.9 NP_001121697.2 Q96H72-1
SLC39A13NM_001128225.3 linkuse as main transcriptc.-14_-12dupCGC 5_prime_UTR_variant 1/10 ENST00000362021.9 NP_001121697.2 Q96H72-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC39A13ENST00000362021.9 linkuse as main transcriptc.-14_-12dupCGC splice_region_variant 1/101 NM_001128225.3 ENSP00000354689.4 Q96H72-1
SLC39A13ENST00000362021.9 linkuse as main transcriptc.-14_-12dupCGC 5_prime_UTR_variant 1/101 NM_001128225.3 ENSP00000354689.4 Q96H72-1

Frequencies

GnomAD3 genomes
AF:
0.300
AC:
44648
AN:
148598
Hom.:
6881
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.222
Gnomad AMI
AF:
0.547
Gnomad AMR
AF:
0.375
Gnomad ASJ
AF:
0.291
Gnomad EAS
AF:
0.289
Gnomad SAS
AF:
0.301
Gnomad FIN
AF:
0.310
Gnomad MID
AF:
0.389
Gnomad NFE
AF:
0.327
Gnomad OTH
AF:
0.317
GnomAD4 exome
AF:
0.410
AC:
548
AN:
1338
Hom.:
110
Cov.:
0
AF XY:
0.416
AC XY:
349
AN XY:
838
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.583
Gnomad4 ASJ exome
AF:
0.400
Gnomad4 EAS exome
AF:
0.463
Gnomad4 SAS exome
AF:
0.353
Gnomad4 NFE exome
AF:
0.467
Gnomad4 OTH exome
AF:
0.500
GnomAD4 genome
AF:
0.301
AC:
44687
AN:
148700
Hom.:
6896
Cov.:
0
AF XY:
0.301
AC XY:
21852
AN XY:
72498
show subpopulations
Gnomad4 AFR
AF:
0.222
Gnomad4 AMR
AF:
0.376
Gnomad4 ASJ
AF:
0.291
Gnomad4 EAS
AF:
0.289
Gnomad4 SAS
AF:
0.300
Gnomad4 FIN
AF:
0.310
Gnomad4 NFE
AF:
0.327
Gnomad4 OTH
AF:
0.324
Asia WGS
AF:
0.274
AC:
937
AN:
3414

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitterclinical testingGeneDxMay 30, 2018- -
Benign, flagged submissionclinical testingGeneDxSep 30, 2016- -

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.

Other links and lift over

dbSNP: rs551004316; hg19: chr11-47430192; API