Variant 20-46724875-C-CGGATGGAT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_030777.4(SLC2A10):c.5-143_5-136dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.80 ( 45595 hom., cov: 0)

Consequence

SLC2A10
NM_030777.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.234

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 20-46724875-C-CGGATGGAT is Benign according to our data. Variant chr20-46724875-C-CGGATGGAT is described in ClinVar as [Benign]. Clinvar id is 1280280.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A10	NM_030777.4 linkuse as main transcript	c.5-143_5-136dup		intron_variant		ENST00000359271.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A10	ENST00000359271.4 linkuse as main transcript	c.5-143_5-136dup		intron_variant		1	NM_030777.4	P1
SLC2A10	ENST00000611837.1 linkuse as main transcript	n.157-143_157-136dup		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.795

AC:

111052

AN:

139612

Hom.:

45577

Cov.:

show subpopulations

Gnomad AFR

AF:

0.576

Gnomad AMI

AF:

0.844

Gnomad AMR

AF:

0.793

Gnomad ASJ

AF:

0.858

Gnomad EAS

AF:

0.872

Gnomad SAS

AF:

0.824

Gnomad FIN

AF:

0.880

Gnomad MID

AF:

0.841

Gnomad NFE

AF:

0.894

Gnomad OTH

AF:

0.812

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.795

AC:

111109

AN:

139726

Hom.:

45595

Cov.:

AF XY:

0.795

AC XY:

53863

AN XY:

67728

show subpopulations

Gnomad4 AFR

AF:

0.576

Gnomad4 AMR

AF:

0.792

Gnomad4 ASJ

AF:

0.858

Gnomad4 EAS

AF:

0.872

Gnomad4 SAS

AF:

0.824

Gnomad4 FIN

AF:

0.880

Gnomad4 NFE

AF:

0.894

Gnomad4 OTH

AF:

0.809

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 14, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over