1-42960950-G-C

Variant names:

• chr1-42960950-G-C
• rs3738515
• ENST00000416689.3:n.546+1373G>C

Variant summary

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

The ENST00000416689.3(SLC2A1-DT):​n.546+1373G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 152,536 control chromosomes in the GnomAD database, including 29,318 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 0.61 (29246 hom., cov: 32)
  • Exomes 𝑓: 0.53 (72 hom.)
• Consequence: SLC2A1-DT ENST00000416689.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181
• Publications: 1 publications found

Genes affected

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

ENSG00000283973 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000416689.3. 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
	SLC2A1-DT	NR_033967.1		n.529+1373G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A1-DT	ENST00000416689.3	TSL:2	n.546+1373G>C		intron	N/A
	SLC2A1-DT	ENST00000431759.7	TSL:2	n.529+1373G>C		intron	N/A
	ENSG00000283973	ENST00000640236.1	TSL:4	n.170+89C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92244 AN: 151844 Hom.: 29196 Cov.: 32

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.588

GnomAD4 exome AF: 0.528 AC: 301 AN: 570 Hom.: 72 AF XY: 0.500 AC XY: 176 AN XY: 352

African (AFR) AF: 0.667 AC: 4 AN: 6

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.700 AC: 7 AN: 10

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.572 AC: 166 AN: 290

Middle Eastern (MID) AF: 0.333 AC: 2 AN: 6

European-Non Finnish (NFE) AF: 0.464 AC: 103 AN: 222

Other (OTH) AF: 0.500 AC: 16 AN: 32

GnomAD4 genome AF: 0.608 AC: 92359 AN: 151966 Hom.: 29246 Cov.: 32 AF XY: 0.614 AC XY: 45561 AN XY: 74234

African (AFR) AF: 0.790 AC: 32783 AN: 41476

American (AMR) AF: 0.658 AC: 10037 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1823 AN: 3462

East Asian (EAS) AF: 0.631 AC: 3243 AN: 5138

South Asian (SAS) AF: 0.640 AC: 3086 AN: 4824

European-Finnish (FIN) AF: 0.559 AC: 5896 AN: 10540

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33770 AN: 67948

Other (OTH) AF: 0.585 AC: 1234 AN: 2110

Alfa AF: 0.389 Hom.: 926

Bravo AF: 0.619

Asia WGS AF: 0.668 AC: 2320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.39
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs3738515; hg19: chr1-43426621; COSMIC: COSV65287064;