20-46724905-GTTTGA-G

Variant summary

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

The NM_030777.4(SLC2A10):c.5-135_5-131del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0063 (7 hom., cov: 0)
  • Exomes 𝑓: 0.0070 (23 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC2A10 NM_030777.4 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.281

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 20-46724905-GTTTGA-G is Benign according to our data. Variant chr20-46724905-GTTTGA-G is described in ClinVar as [Likely_benign]. Clinvar id is 1190224.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00626 (929/148440) while in subpopulation NFE AF= 0.0107 (710/66664). AF 95% confidence interval is 0.01. There are 7 homozygotes in gnomad4. There are 428 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A10	NM_030777.4	c.5-135_5-131del		intron_variant		ENST00000359271.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A10	ENST00000359271.4	c.5-135_5-131del		intron_variant		1	NM_030777.4	P1
SLC2A10	ENST00000611837.1	n.157-135_157-131del		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.00626 AC: 929 AN: 148328 Hom.: 7 Cov.: 0

Gnomad AFR AF: 0.00112

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00486

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00905

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0106

Gnomad OTH AF: 0.00443

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00695 AC: 6740 AN: 969412 Hom.: 23 AF XY: 0.00655 AC XY: 3239 AN XY: 494430

Gnomad4 AFR exome AF: 0.00207

Gnomad4 AMR exome AF: 0.00651

Gnomad4 ASJ exome AF: 0.000595

Gnomad4 EAS exome AF: 0.000146

Gnomad4 SAS exome AF: 0.000379

Gnomad4 FIN exome AF: 0.00995

Gnomad4 NFE exome AF: 0.00825

Gnomad4 OTH exome AF: 0.00589

GnomAD4 genome AF: 0.00626 AC: 929 AN: 148440 Hom.: 7 Cov.: 0 AF XY: 0.00591 AC XY: 428 AN XY: 72412

Gnomad4 AFR AF: 0.00111

Gnomad4 AMR AF: 0.00485

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00905

Gnomad4 NFE AF: 0.0107

Gnomad4 OTH AF: 0.00439

Alfa AF: 0.0105 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

Aug 06, 2019

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs375425716; hg19: chr20-45353544;