chr20-46736010-T-C

Variant names:

• chr20-46736010-T-C
• rs1059217
• NM_030777.4:c.*2176T>C

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_030777.4(SLC2A10):​c.*2176T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 152,024 control chromosomes in the GnomAD database, including 12,967 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.41 (12967 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: SLC2A10 NM_030777.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -2.46
• Publications: 11 publications found

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]

SLC2A10 Gene-Disease associations (from GenCC):

• arterial tortuosity syndrome

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: PanelApp Australia, G2P, Orphanet, Labcorp Genetics (formerly Invitae), ClinGen, Ambry Genetics, Genomics England PanelApp

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BP6: Variant 20-46736010-T-C is Benign according to our data. Variant chr20-46736010-T-C is described in ClinVar as Benign. ClinVar VariationId is 338631.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030777.4. 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
	SLC2A10	NM_030777.4	MANE Select	c.*2176T>C		3_prime_UTR	Exon 5 of 5	NP_110404.1	O95528

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A10	ENST00000359271.4	TSL:1 MANE Select	c.*2176T>C		3_prime_UTR	Exon 5 of 5	ENSP00000352216.2	O95528
	SLC2A10	ENST00000862794.1		c.*2176T>C		3_prime_UTR	Exon 5 of 5	ENSP00000532853.1
	SLC2A10	ENST00000862792.1		c.*2176T>C		3_prime_UTR	Exon 6 of 6	ENSP00000532851.1

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61697 AN: 151908 Hom.: 12958 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.424

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.406 AC: 61736 AN: 152024 Hom.: 12967 Cov.: 32 AF XY: 0.411 AC XY: 30525 AN XY: 74306

African (AFR) AF: 0.317 AC: 13150 AN: 41494

American (AMR) AF: 0.457 AC: 6978 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1541 AN: 3464

East Asian (EAS) AF: 0.603 AC: 3118 AN: 5168

South Asian (SAS) AF: 0.400 AC: 1927 AN: 4816

European-Finnish (FIN) AF: 0.456 AC: 4802 AN: 10536

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.425 AC: 28886 AN: 67952

Other (OTH) AF: 0.426 AC: 900 AN: 2112

Alfa AF: 0.411 Hom.: 6195

Bravo AF: 0.403

Asia WGS AF: 0.463 AC: 1609 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	1	Arterial tortuosity syndrome (1)
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.16
DANN	Benign	0.35
PhyloP100		-2.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1059217; hg19: chr20-45364649;