rs1399925

Variant names:

• chr21-42571832-A-G
• rs1399925
• NM_001320537.2:c.1424-2986A>G

Your query was ambiguous. Multiple possible variants found:

• chr21-42571832-A-G
• chr21-42571832-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001320537.2(SLC37A1):​c.1424-2986A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.74 in 151,994 control chromosomes in the GnomAD database, including 42,580 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 0.74 (42580 hom., cov: 31)
• Consequence: SLC37A1 NM_001320537.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• Publications: 3 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.804 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC37A1	NM_001320537.2	MANE Select	c.1424-2986A>G		intron	N/A	NP_001307466.1	P57057
	SLC37A1	NM_018964.4		c.1424-2986A>G		intron	N/A	NP_061837.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC37A1	ENST00000352133.3	TSL:1 MANE Select	c.1424-2986A>G		intron	N/A	ENSP00000344648.2	P57057
	SLC37A1	ENST00000398341.7	TSL:1	c.1424-2986A>G		intron	N/A	ENSP00000381383.3	P57057
	SLC37A1	ENST00000893156.1		c.1523-2986A>G		intron	N/A	ENSP00000563215.1

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112411 AN: 151876 Hom.: 42546 Cov.: 31

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.849

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.729

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

GnomAD4 genome AF: 0.740 AC: 112508 AN: 151994 Hom.: 42580 Cov.: 31 AF XY: 0.733 AC XY: 54488 AN XY: 74296

African (AFR) AF: 0.811 AC: 33628 AN: 41444

American (AMR) AF: 0.798 AC: 12199 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2388 AN: 3470

East Asian (EAS) AF: 0.195 AC: 1004 AN: 5160

South Asian (SAS) AF: 0.614 AC: 2960 AN: 4824

European-Finnish (FIN) AF: 0.722 AC: 7619 AN: 10548

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.739 AC: 50223 AN: 67950

Other (OTH) AF: 0.725 AC: 1535 AN: 2116

Alfa AF: 0.733 Hom.: 5027

Bravo AF: 0.749

Asia WGS AF: 0.452 AC: 1572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.28
PhyloP100		0.0090
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: rs1399925; hg19: chr21-43991942;