rs11537640

Variant names:

• chr1-42958848-T-A
• rs11537640
• NM_006516.4:c.-197A>T

Your query was ambiguous. Multiple possible variants found:

• chr1-42958848-T-A
• chr1-42958848-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_006516.4(SLC2A1):​c.-197A>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000238 in 420,048 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0000024 (0 hom.)
• Consequence: SLC2A1 NM_006516.4 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 14 publications found

Genes affected

SLC2A1 (HGNC:11005): (solute carrier family 2 member 1) This gene encodes a major glucose transporter in the mammalian blood-brain barrier. The encoded protein is found primarily in the cell membrane and on the cell surface, where it can also function as a receptor for human T-cell leukemia virus (HTLV) I and II. Mutations in this gene have been found in a family with paroxysmal exertion-induced dyskinesia. [provided by RefSeq, Apr 2013]

SLC2A1-DT (HGNC:44187): (SLC2A1 divergent transcript)

ENSG00000283973 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A1	NM_006516.4	c.-197A>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 10	ENST00000426263.10	NP_006507.2
SLC2A1	NM_006516.4	c.-197A>T		5_prime_UTR_variant	Exon 1 of 10	ENST00000426263.10	NP_006507.2
SLC2A1-DT	NR_033967.1	n.-201T>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A1	ENST00000426263.10	c.-197A>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 10	1	NM_006516.4	ENSP00000416293.2
SLC2A1	ENST00000426263.10	c.-197A>T		5_prime_UTR_variant	Exon 1 of 10	1	NM_006516.4	ENSP00000416293.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000238 AC: 1 AN: 420048 Hom.: 0 Cov.: 5 AF XY: 0.00000446 AC XY: 1 AN XY: 224212

African (AFR) AF: 0.00 AC: 0 AN: 9180

American (AMR) AF: 0.00 AC: 0 AN: 18692

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12602

East Asian (EAS) AF: 0.00 AC: 0 AN: 25692

South Asian (SAS) AF: 0.00 AC: 0 AN: 44690

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 28466

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3200

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 253658

Other (OTH) AF: 0.0000419 AC: 1 AN: 23868

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	5.3
DANN	Benign	0.66
PhyloP100		-1.7
PromoterAI		-0.12	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs11537640; hg19: chr1-43424519;