rs35112095

Variant names:

• chr21-42569923-G-A
• rs35112095
• NM_001320537.2:c.1423+1485G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 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=-0.91).
• 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 rank	MANE	Protein	UniProt
SLC37A1	NM_001320537.2	c.1423+1485G>A		intron_variant	Intron 17 of 19	ENST00000352133.3	NP_001307466.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC37A1	ENST00000352133.3	c.1423+1485G>A		intron_variant	Intron 17 of 19	1	NM_001320537.2	ENSP00000344648.2
SLC37A1	ENST00000398341.7	c.1423+1485G>A		intron_variant	Intron 18 of 20	1		ENSP00000381383.3
SLC37A1	ENST00000496416.1	n.202+1485G>A		intron_variant	Intron 3 of 4	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

African (AFR) AF: 0.00976 AC: 406 AN: 41584

American (AMR) AF: 0.0230 AC: 352 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0135 AC: 47 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5186

South Asian (SAS) AF: 0.0120 AC: 58 AN: 4832

European-Finnish (FIN) AF: 0.0179 AC: 190 AN: 10624

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0522 AC: 3550 AN: 68038

Other (OTH) AF: 0.0260 AC: 55 AN: 2116

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
PhyloP100		-0.94
Mutation Taster		=100/0	polymorphism

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: rs35112095; hg19: chr21-43990033;