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. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001320537.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC37A1	NM_001320537.2	MANE Select	c.57-1655G>A		intron	N/A	NP_001307466.1
	SLC37A1	NM_018964.4		c.57-1655G>A		intron	N/A	NP_061837.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC37A1	ENST00000352133.3	TSL:1 MANE Select	c.57-1655G>A		intron	N/A	ENSP00000344648.2
	SLC37A1	ENST00000398341.7	TSL:1	c.57-1655G>A		intron	N/A	ENSP00000381383.3
	SLC37A1	ENST00000471277.5	TSL:1	n.355-1655G>A		intron	N/A

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

African (AFR) AF: 0.448 AC: 18518 AN: 41350

American (AMR) AF: 0.619 AC: 9453 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1467 AN: 3468

East Asian (EAS) AF: 0.358 AC: 1844 AN: 5148

South Asian (SAS) AF: 0.443 AC: 2134 AN: 4814

European-Finnish (FIN) AF: 0.415 AC: 4375 AN: 10538

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31512 AN: 67916

Other (OTH) AF: 0.465 AC: 980 AN: 2106

Alfa AF: 0.470 Hom.: 28541

Bravo AF: 0.482

Asia WGS AF: 0.395 AC: 1376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.13
DANN	Benign	0.73
PhyloP100		-0.83
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs875060; hg19: chr21-43944231;