dbSNP rs56765672: SLC3A2:c.-161G>A (chr11-62856109-G-A) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2

The ENST00000377890.6(SLC3A2):c.-161G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000809 in 568,648 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000079 ( 0 hom., cov: 33)

Exomes 𝑓: 0.000082 ( 0 hom. )

Consequence

SLC3A2
ENST00000377890.6 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.413

Publications

0 publications found

Variant links:

Genes affected

SLC3A2 (HGNC:11026): (solute carrier family 3 member 2) This gene is a member of the solute carrier family and encodes a cell surface, transmembrane protein. The protein exists as the heavy chain of a heterodimer, covalently bound through di-sulfide bonds to one of several possible light chains. The encoded transporter plays a role in regulation of intracellular calcium levels and transports L-type amino acids. Alternatively spliced transcript variants, encoding different isoforms, have been characterized. [provided by RefSeq, Nov 2010]

SLC3A2 links:

SNHG1 (HGNC:32688): (small nucleolar RNA host gene 1) This locus represents a small nucleolar RNA host gene that produces multiple alternatively spliced long non-coding RNAs. This gene is upregulated in cancers and is thought to act as promoter of cell proliferation. This transcript negatively regulates tumor suppressor genes such as tumor protein p53. Expression of this locus may be a marker of tumor progression. [provided by RefSeq, Dec 2017]

SNHG1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BS2

High AC in GnomAd4 at 12 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein	UniProt
SLC3A2	NM_001012662.3 link	c.-161G>A	5_prime_UTR_variant	Exon 1 of 12	NP_001012680.1	P08195-5
SLC3A2	NM_002394.6 link	c.-161G>A	5_prime_UTR_variant	Exon 1 of 12	NP_002385.3	P08195-1
SLC3A2	NM_001012664.3 link	c.-161G>A	5_prime_UTR_variant	Exon 1 of 10	NP_001012682.1	P08195-3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
SLC3A2	ENST00000377890.6 link	c.-161G>A	5_prime_UTR_variant	Exon 1 of 12	1	ENSP00000367122.2	P08195-1
SLC3A2	ENST00000680002.1 link	n.-161G>A	non_coding_transcript_exon_variant	Exon 1 of 13		ENSP00000506366.1	A0A7P0TAT7
SLC3A2	ENST00000538084.2 link	c.-161G>A	5_prime_UTR_variant	Exon 1 of 13	3	ENSP00000440001.2	P08195-4H0YFS2

Frequencies

GnomAD3 genomes

AF:

0.0000788

AC:

AN:

152250

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000196

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000103

Gnomad OTH

AF:

0.000955

GnomAD4 exome

AF:

0.0000817

AC:

AN:

416398

Hom.:

Cov.:

AF XY:

0.0000685

AC XY:

AN XY:

218876

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

11262

American (AMR)

AF:

0.000153

AC:

AN:

13078

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

12406

East Asian (EAS)

AF:

0.00

AC:

AN:

28306

South Asian (SAS)

AF:

0.00

AC:

AN:

35164

European-Finnish (FIN)

AF:

0.00

AC:

AN:

29012

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1728

European-Non Finnish (NFE)

AF:

0.000111

AC:

AN:

261490

Other (OTH)

AF:

0.000125

AC:

AN:

23952

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000788

AC:

AN:

152250

Hom.:

Cov.:

AF XY:

0.0000672

AC XY:

AN XY:

74380

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

41472

American (AMR)

AF:

0.000196

AC:

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5200

South Asian (SAS)

AF:

0.00

AC:

AN:

4836

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10624

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.000103

AC:

AN:

68040

Other (OTH)

AF:

0.000955

AC:

AN:

2094

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.546

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.0000907

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

(source)

DANN

Benign

0.90

PhyloP100

0.41

PromoterAI

-0.089

Neutral

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over