rs35112095

Positions:

• chr21-42569923-G-A

Variant summary

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

The NM_001320537.2(SLC37A1):​c.1423+1485G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0309 in 152,358 control chromosomes in the GnomAD database, including 99 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 0.031 (99 hom., cov: 35)
• Consequence: SLC37A1 NM_001320537.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.940

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]

SLC37A1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC37A1	NM_001320537.2	c.1423+1485G>A		intron_variant		ENST00000352133.3	NP_001307466.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC37A1	ENST00000352133.3	c.1423+1485G>A		intron_variant		1	NM_001320537.2	ENSP00000344648.2
SLC37A1	ENST00000398341.7	c.1423+1485G>A		intron_variant		1		ENSP00000381383.3
SLC37A1	ENST00000496416.1	n.202+1485G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0309 AC: 4707 AN: 152240 Hom.: 99 Cov.: 35

Gnomad AFR AF: 0.00982

Gnomad AMI AF: 0.0507

Gnomad AMR AF: 0.0230

Gnomad ASJ AF: 0.0135

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0116

Gnomad FIN AF: 0.0179

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0522

Gnomad OTH AF: 0.0263

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

GnomAD4 genome AF: 0.0309 AC: 4708 AN: 152358 Hom.: 99 Cov.: 35 AF XY: 0.0283 AC XY: 2112 AN XY: 74504

Gnomad4 AFR AF: 0.00976

Gnomad4 AMR AF: 0.0230

Gnomad4 ASJ AF: 0.0135

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0120

Gnomad4 FIN AF: 0.0179

Gnomad4 NFE AF: 0.0522

Gnomad4 OTH AF: 0.0260

Alfa AF: 0.0371 Hom.: 22

Bravo AF: 0.0303

Asia WGS AF: 0.00635 AC: 23 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.80
DANN	Benign	0.61

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: rs35112095; hg19: chr21-43990033;