dbSNP rs7700790: ENSG00000253897:n.951-120C>A (chr5-151366778-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000517788.1(ENSG00000253897):n.951-120C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 153,038 control chromosomes in the GnomAD database, including 4,236 homozygotes. 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 0.14 ( 4236 hom., cov: 32)

Exomes 𝑓: 0.017 ( 0 hom. )

Consequence

ENSG00000253897
ENST00000517788.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.50

Publications

2 publications found

Variant links:

Genes affected

ENSG00000253897 (HGNC:):

ENSG00000253897 links:

SLC36A1 (HGNC:18761): (solute carrier family 36 member 1) This gene encodes a member of the eukaryote-specific amino acid/auxin permease (AAAP) 1 transporter family. The encoded protein functions as a proton-dependent, small amino acid transporter. This gene is clustered with related family members on chromosome 5q33.1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]

SLC36A1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
SLC36A1	XM_011537591.2 link	c.-90+22044G>T	intron_variant	Intron 1 of 11	XP_011535893.1
LOC105378234	XR_007059004.1 link	n.1345-13972C>A	intron_variant	Intron 6 of 6
LOC105378234	XR_007059005.1 link	n.1127-120C>A	intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000253897	ENST00000517788.1 link	n.951-120C>A	intron_variant	Intron 8 of 8	6
ENSG00000290991	ENST00000647906.1 link	n.1057-120C>A	intron_variant	Intron 3 of 3
ENSG00000297368	ENST00000747508.1 link	n.675+22044G>T	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.141

AC:

21392

AN:

152078

Hom.:

4221

Cov.:

show subpopulations

Gnomad AFR

AF:

0.445

Gnomad AMI

AF:

0.0692

Gnomad AMR

AF:

0.0613

Gnomad ASJ

AF:

0.0193

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.0259

Gnomad FIN

AF:

0.0196

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0201

Gnomad OTH

AF:

0.106

GnomAD4 exome

AF:

0.0166

AC:

AN:

842

Hom.:

AF XY:

0.0207

AC XY:

AN XY:

482

show subpopulations

African (AFR)

AF:

0.200

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.0250

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00980

AC:

AN:

612

Other (OTH)

AF:

0.0741

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

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:

0.141

AC:

21449

AN:

152196

Hom.:

4236

Cov.:

AF XY:

0.136

AC XY:

10157

AN XY:

74414

show subpopulations

African (AFR)

AF:

0.445

AC:

18453

AN:

41472

American (AMR)

AF:

0.0611

AC:

935

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0193

AC:

AN:

3470

East Asian (EAS)

AF:

0.000193

AC:

AN:

5184

South Asian (SAS)

AF:

0.0257

AC:

124

AN:

4820

European-Finnish (FIN)

AF:

0.0196

AC:

208

AN:

10608

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0200

AC:

1364

AN:

68030

Other (OTH)

AF:

0.105

AC:

223

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

664

1328

1993

2657

3321

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

186

372

558

744

930

<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:

0.107

Hom.:

406

Bravo

AF:

0.158

Asia WGS

AF:

0.0340

AC:

118

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.5

(source)

DANN

Benign

0.25

PhyloP100

-1.5

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