chr20-46724918-G-GT

Position:

• chr20-46724918-G-GT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The NM_030777.4(SLC2A10):​c.5-121dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00619 in 1,212,124 control chromosomes in the GnomAD database, including 33 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0069 (7 hom., cov: 33)
  • Exomes 𝑓: 0.0061 (26 hom.)
• Consequence: SLC2A10 NM_030777.4 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.14

Genes affected

SLC2A10 (HGNC:13444): (solute carrier family 2 member 10) This gene encodes a member of the class III facilitative glucose transporter family. The encoded protein plays a role in regulation of glucose homeostasis. Mutations in this gene have been associated with arterial tortuosity syndrome.[provided by RefSeq, Dec 2009]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 20-46724918-G-GT is Benign according to our data. Variant chr20-46724918-G-GT is described in ClinVar as [Likely_benign]. Clinvar id is 676785.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00686 (935/136280) while in subpopulation NFE AF= 0.0112 (714/63750). AF 95% confidence interval is 0.0105. There are 7 homozygotes in gnomad4. There are 433 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A10	NM_030777.4	c.5-121dup		intron_variant		ENST00000359271.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A10	ENST00000359271.4	c.5-121dup		intron_variant		1	NM_030777.4	P1
SLC2A10	ENST00000611837.1	n.157-121dup		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.00687 AC: 935 AN: 136182 Hom.: 7 Cov.: 33

Gnomad AFR AF: 0.00126

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00546

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0104

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0112

Gnomad OTH AF: 0.00486

GnomAD4 exome AF: 0.00610 AC: 6566 AN: 1075844 Hom.: 26 AF XY: 0.00587 AC XY: 3194 AN XY: 543978

Gnomad4 AFR exome AF: 0.000934

Gnomad4 AMR exome AF: 0.00639

Gnomad4 ASJ exome AF: 0.0000893

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00986

Gnomad4 NFE exome AF: 0.00713

Gnomad4 OTH exome AF: 0.00535

GnomAD4 genome AF: 0.00686 AC: 935 AN: 136280 Hom.: 7 Cov.: 33 AF XY: 0.00655 AC XY: 433 AN XY: 66094

Gnomad4 AFR AF: 0.00126

Gnomad4 AMR AF: 0.00546

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.0104

Gnomad4 NFE AF: 0.0112

Gnomad4 OTH AF: 0.00481

Alfa AF: 0.00655 Hom.: 2

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 14, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs879560987; hg19: chr20-45353557;