1-42964413-C-T

Variant names:

• chr1-42964413-C-T
• rs841839
• ENST00000416689.2:n.505+4836C>T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000416689.2(SLC2A1-DT):​n.505+4836C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 28)
• Consequence: SLC2A1-DT ENST00000416689.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

Genes affected

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

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A1-DT	NR_033967.1	n.529+4836C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A1-DT	ENST00000416689.2	n.505+4836C>T		intron_variant	Intron 1 of 2	2
SLC2A1-DT	ENST00000431759.6	n.529+4836C>T		intron_variant	Intron 1 of 3	2
SLC2A1-DT	ENST00000653200.1	n.500+4836C>T		intron_variant	Intron 1 of 3
SLC2A1-DT	ENST00000664148.1	n.478+4836C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes Cov.: 28

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

GnomAD4 genome Cov.: 28

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	1.1
DANN	Benign	0.95

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs841839; hg19: chr1-43430084;