rs3738514

Variant names:

• chr1-42960920-C-T
• rs3738514
• ENST00000416689.3:n.546+1343C>T

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+1343C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 152,886 control chromosomes in the GnomAD database, including 3,654 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 0.22 (3639 hom., cov: 32)
  • Exomes 𝑓: 0.18 (15 hom.)
• Consequence: SLC2A1-DT ENST00000416689.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.844
• Publications: 8 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.236 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+1343C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A1-DT	ENST00000416689.3	TSL:2	n.546+1343C>T		intron	N/A
	SLC2A1-DT	ENST00000431759.7	TSL:2	n.529+1343C>T		intron	N/A
	ENSG00000283973	ENST00000640236.1	TSL:4	n.170+119G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32746 AN: 152050 Hom.: 3638 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.213

GnomAD4 exome AF: 0.184 AC: 132 AN: 716 Hom.: 15 AF XY: 0.164 AC XY: 72 AN XY: 438

African (AFR) AF: 0.00 AC: 0 AN: 8

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 10

South Asian (SAS) AF: 0.250 AC: 2 AN: 8

European-Finnish (FIN) AF: 0.217 AC: 81 AN: 374

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.151 AC: 42 AN: 278

Other (OTH) AF: 0.176 AC: 6 AN: 34

GnomAD4 genome AF: 0.215 AC: 32772 AN: 152170 Hom.: 3639 Cov.: 32 AF XY: 0.219 AC XY: 16277 AN XY: 74392

African (AFR) AF: 0.207 AC: 8576 AN: 41524

American (AMR) AF: 0.242 AC: 3706 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 800 AN: 3468

East Asian (EAS) AF: 0.213 AC: 1100 AN: 5162

South Asian (SAS) AF: 0.207 AC: 997 AN: 4818

European-Finnish (FIN) AF: 0.248 AC: 2621 AN: 10586

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14292 AN: 67996

Other (OTH) AF: 0.214 AC: 453 AN: 2114

Alfa AF: 0.211 Hom.: 1089

Bravo AF: 0.213

Asia WGS AF: 0.226 AC: 787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.70
PhyloP100		-0.84

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3738514;

hg19: chr1-43426591;