8-22404458-G-GTT

Variant names:

• chr8-22404458-G-GTT
• rs375772752
• NM_001128431.4:c.-15-236_-15-235dupTT

Variant summary

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

The NM_001128431.4(SLC39A14):​c.-15-236_-15-235dupTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00012 in 157,816 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 0.0044 (11 hom., cov: 0)
  • Exomes 𝑓: 0.00012 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC39A14 NM_001128431.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43

Genes affected

SLC39A14 (HGNC:20858): (solute carrier family 39 member 14) This gene encodes a member of the the SLC39A family of divalent metal transporters that mediates the cellular uptake of manganese, zinc, iron, and cadmium. The encoded protein contains eight transmembrane domains, a histidine-rich motif, and a metalloprotease motif, and is expressed on the plasma membrane and the endocytic vesicle membrane. It is an important transporter of nontransferrin-bound iron and a critical regulator of manganese homeostasis. Naturally occurring mutations in this gene are associated with neurodegeneration with brain iron accumulation and early-onset parkinsonism-dystonia with hypermanganesemia. [provided by RefSeq, May 2017]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS1: Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.00012 (19/157816) while in subpopulation AMR AF= 0.000186 (1/5366). AF 95% confidence interval is 0.0000595. There are 0 homozygotes in gnomad4_exome. There are 8 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC39A14	NM_001128431.4	c.-15-236_-15-235dupTT		intron_variant	Intron 1 of 8	ENST00000381237.6	NP_001121903.1
SLC39A14	NM_015359.6	c.-15-236_-15-235dupTT		intron_variant	Intron 1 of 8	ENST00000359741.10	NP_056174.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC39A14	ENST00000359741.10	c.-15-238_-15-237insTT		intron_variant	Intron 1 of 8	2	NM_015359.6	ENSP00000352779.5
SLC39A14	ENST00000381237.6	c.-15-238_-15-237insTT		intron_variant	Intron 1 of 8	1	NM_001128431.4	ENSP00000370635.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 546 AN: 122738 Hom.: 11 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.0141

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00364

Gnomad ASJ AF: 0.00193

Gnomad EAS AF: 0.000822

Gnomad SAS AF: 0.000522

Gnomad FIN AF: 0.000471

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00109

Gnomad OTH AF: 0.00117

GnomAD4 exome AF: 0.000120 AC: 19 AN: 157816 Hom.: 0 AF XY: 0.0000978 AC XY: 8 AN XY: 81818

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000186

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000802

Gnomad4 SAS exome AF: 0.000112

Gnomad4 FIN exome AF: 0.000278

Gnomad4 NFE exome AF: 0.000107

Gnomad4 OTH exome AF: 0.000209

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00444 AC: 545 AN: 122774 Hom.: 11 Cov.: 0 AF XY: 0.00408 AC XY: 239 AN XY: 58630

Gnomad4 AFR AF: 0.0140

Gnomad4 AMR AF: 0.00364

Gnomad4 ASJ AF: 0.00193

Gnomad4 EAS AF: 0.000823

Gnomad4 SAS AF: 0.000524

Gnomad4 FIN AF: 0.000471

Gnomad4 NFE AF: 0.00109

Gnomad4 OTH AF: 0.00116

Alfa AF: 0.0000864 Hom.: 50

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: rs375772752; hg19: chr8-22261971;