NM_030777.4:c.1547+96C>T

Variant names:

• chr20-46729584-C-T
• rs2425907
• NM_030777.4:c.1547+96C>T

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.1547+96C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 1,313,316 control chromosomes in the GnomAD database, including 126,068 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.38 (11408 hom., cov: 27)
  • Exomes 𝑓: 0.45 (114660 hom.)
• Consequence: SLC2A10 NM_030777.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.113
• Publications: 6 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=-0.85).
• BP6: Variant 20-46729584-C-T is Benign according to our data. Variant chr20-46729584-C-T is described in ClinVar as Benign. ClinVar VariationId is 673813.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 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.1547+96C>T		intron	N/A	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.1547+96C>T		intron	N/A	ENSP00000352216.2	O95528
	SLC2A10	ENST00000862794.1		c.1841+96C>T		intron	N/A	ENSP00000532853.1
	SLC2A10	ENST00000862792.1		c.1679+96C>T		intron	N/A	ENSP00000532851.1

Frequencies

GnomAD3 genomes AF: 0.383 AC: 55843 AN: 145736 Hom.: 11399 Cov.: 27

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.415

GnomAD4 exome AF: 0.453 AC: 528404 AN: 1167498 Hom.: 114660 AF XY: 0.449 AC XY: 264784 AN XY: 589408

African (AFR) AF: 0.240 AC: 6192 AN: 25768

American (AMR) AF: 0.439 AC: 17573 AN: 40034

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 10593 AN: 21976

East Asian (EAS) AF: 0.651 AC: 22398 AN: 34420

South Asian (SAS) AF: 0.355 AC: 28100 AN: 79246

European-Finnish (FIN) AF: 0.493 AC: 19748 AN: 40046

Middle Eastern (MID) AF: 0.435 AC: 1665 AN: 3830

European-Non Finnish (NFE) AF: 0.458 AC: 399916 AN: 873986

Other (OTH) AF: 0.461 AC: 22219 AN: 48192

GnomAD4 genome AF: 0.383 AC: 55874 AN: 145818 Hom.: 11408 Cov.: 27 AF XY: 0.389 AC XY: 27421 AN XY: 70552

African (AFR) AF: 0.224 AC: 8800 AN: 39240

American (AMR) AF: 0.456 AC: 6653 AN: 14576

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1484 AN: 3456

East Asian (EAS) AF: 0.614 AC: 2991 AN: 4872

South Asian (SAS) AF: 0.355 AC: 1605 AN: 4526

European-Finnish (FIN) AF: 0.489 AC: 4367 AN: 8932

Middle Eastern (MID) AF: 0.404 AC: 110 AN: 272

European-Non Finnish (NFE) AF: 0.428 AC: 28703 AN: 67050

Other (OTH) AF: 0.417 AC: 840 AN: 2014

Alfa AF: 0.402 Hom.: 34211

Bravo AF: 0.370

Asia WGS AF: 0.426 AC: 1479 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.90
DANN	Benign	0.62
PhyloP100		0.11
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: rs2425907; hg19: chr20-45358223; COSMIC: COSV63715860; COSMIC: COSV63715860;