rs875060

Variant names:

• chr21-42524121-G-A
• rs875060
• NM_001320537.2:c.57-1655G>A

Your query was ambiguous. Multiple possible variants found:

• chr21-42524121-G-A
• chr21-42524121-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001320537.2(SLC37A1):​c.57-1655G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 151,810 control chromosomes in the GnomAD database, including 16,847 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.47 (16847 hom., cov: 30)
• Consequence: SLC37A1 NM_001320537.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.835

Genes affected

SLC37A1 (HGNC:11024): (solute carrier family 37 member 1) The protein encoded by this gene localizes to the endoplasmic reticulum (ER) membrane. This protein translocates glucose-6-phosphate from the cytoplasm into the lumen of the ER for hydrolysis into glucose by another ER membrane protein. This gene is a member of the solute carrier 37 gene family. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC37A1	NM_001320537.2	c.57-1655G>A		intron_variant	Intron 2 of 19	ENST00000352133.3	NP_001307466.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC37A1	ENST00000352133.3	c.57-1655G>A		intron_variant	Intron 2 of 19	1	NM_001320537.2	ENSP00000344648.2
SLC37A1	ENST00000398341.7	c.57-1655G>A		intron_variant	Intron 3 of 20	1		ENSP00000381383.3
SLC37A1	ENST00000471277.5	n.355-1655G>A		intron_variant	Intron 3 of 3	1

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70821 AN: 151692 Hom.: 16831 Cov.: 30

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.472

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.467 AC: 70884 AN: 151810 Hom.: 16847 Cov.: 30 AF XY: 0.466 AC XY: 34564 AN XY: 74186

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.465

Alfa AF: 0.468 Hom.: 22543

Bravo AF: 0.482

Asia WGS AF: 0.395 AC: 1376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.13
DANN	Benign	0.73

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: rs875060; hg19: chr21-43944231;