3-39383488-G-A

Variant names:

• chr3-39383488-G-A
• rs527536267
• NM_017875.4:c.-237G>A

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_Strong BS1_Supporting

The NM_017875.4(SLC25A38):​c.-237G>A variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000823 in 570,192 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.00083 (1 hom., cov: 33)
  • Exomes 𝑓: 0.00082 (1 hom.)
• Consequence: SLC25A38 NM_017875.4 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Uncertain significance criteria provided, single submitter U:2
• Conservation: PhyloP100: 0.599

Genes affected

SLC25A38 (HGNC:26054): (solute carrier family 25 member 38) This gene is a member of the mitochondrial carrier family. The encoded protein is required during erythropoiesis and is important for the biosynthesis of heme. Mutations in this gene are the cause of autosomal congenital sideroblastic anemia (anemia, sideroblastic, 2, pyridoxine-refractory). A related pseudogene is found on chromosome 1. [provided by RefSeq, Aug 2017]

ENSG00000287780 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.000834 (127/152252) while in subpopulation AMR AF= 0.00294 (45/15292). AF 95% confidence interval is 0.00226. There are 1 homozygotes in gnomad4. There are 53 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC25A38	NM_017875.4	c.-237G>A		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 7	ENST00000650617.1	NP_060345.2
SLC25A38	NM_017875.4	c.-237G>A		5_prime_UTR_variant	Exon 1 of 7	ENST00000650617.1	NP_060345.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC25A38	ENST00000650617	c.-237G>A		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 7		NM_017875.4	ENSP00000497532.1
SLC25A38	ENST00000650617	c.-237G>A		5_prime_UTR_variant	Exon 1 of 7		NM_017875.4	ENSP00000497532.1

Frequencies

GnomAD3 genomes AF: 0.000834 AC: 127 AN: 152252 Hom.: 1 Cov.: 33

Gnomad AFR AF: 0.000121

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00294

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: 0.00112

Gnomad OTH AF: 0.000478

GnomAD4 exome AF: 0.000818 AC: 342 AN: 417940 Hom.: 1 Cov.: 3 AF XY: 0.000803 AC XY: 178 AN XY: 221802

Gnomad4 AFR exome AF: 0.0000867

Gnomad4 AMR exome AF: 0.00109

Gnomad4 ASJ exome AF: 0.0000801

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000222

Gnomad4 FIN exome AF: 0.0000707

Gnomad4 NFE exome AF: 0.00122

Gnomad4 OTH exome AF: 0.000421

GnomAD4 genome AF: 0.000834 AC: 127 AN: 152252 Hom.: 1 Cov.: 33 AF XY: 0.000713 AC XY: 53 AN XY: 74378

Gnomad4 AFR AF: 0.000121

Gnomad4 AMR AF: 0.00294

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00112

Gnomad4 OTH AF: 0.000478

Alfa AF: 0.000624 Hom.: 0

Bravo AF: 0.000740

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:2

Revision: criteria provided, single submitter

Submissions by phenotype

X-linked sideroblastic anemia 1 Uncertain:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Sideroblastic anemia 2 Uncertain:1

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	9.6
DANN	Benign	0.82

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs527536267; hg19: chr3-39424979;