Genetic Variant SLC36A1:c.-90+21739A>G (chr5-151366473-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000647906.1(ENSG00000290991):n.1242T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.381 in 285,402 control chromosomes in the GnomAD database, including 21,636 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 0.37 ( 10548 hom., cov: 32)

Exomes 𝑓: 0.39 ( 11088 hom. )

Consequence

ENSG00000290991
ENST00000647906.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.155

Publications

7 publications found

Variant links:

Genes affected

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:

ENSG00000253897 (HGNC:):

ENSG00000253897 links:

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new If you want to explore the variant's impact on the transcript ENST00000647906.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.66).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647906.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
ENSG00000253897	ENST00000517788.1	TSL:6	n.1136T>C	non_coding_transcript_exon	Exon 9 of 9
ENSG00000290991	ENST00000647906.1		n.1242T>C	non_coding_transcript_exon	Exon 4 of 4
ENSG00000297368	ENST00000747508.1		n.675+21739A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.370

AC:

56193

AN:

151936

Hom.:

10544

Cov.:

show subpopulations

Gnomad AFR

AF:

0.349

Gnomad AMI

AF:

0.345

Gnomad AMR

AF:

0.270

Gnomad ASJ

AF:

0.386

Gnomad EAS

AF:

0.427

Gnomad SAS

AF:

0.433

Gnomad FIN

AF:

0.452

Gnomad MID

AF:

0.288

Gnomad NFE

AF:

0.384

Gnomad OTH

AF:

0.354

GnomAD4 exome

AF:

0.394

AC:

52525

AN:

133348

Hom.:

11088

Cov.:

AF XY:

0.400

AC XY:

31392

AN XY:

78564

show subpopulations

African (AFR)

AF:

0.339

AC:

818

AN:

2416

American (AMR)

AF:

0.208

AC:

1393

AN:

6700

Ashkenazi Jewish (ASJ)

AF:

0.364

AC:

1114

AN:

3060

East Asian (EAS)

AF:

0.439

AC:

1100

AN:

2506

South Asian (SAS)

AF:

0.428

AC:

9265

AN:

21628

European-Finnish (FIN)

AF:

0.451

AC:

7780

AN:

17232

Middle Eastern (MID)

AF:

0.249

AC:

178

AN:

714

European-Non Finnish (NFE)

AF:

0.392

AC:

28652

AN:

73038

Other (OTH)

AF:

0.368

AC:

2225

AN:

6054

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1311

2623

3934

5246

6557

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

164

246

328

410

<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:

0.370

AC:

56235

AN:

152054

Hom.:

10548

Cov.:

AF XY:

0.371

AC XY:

27552

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.349

AC:

14460

AN:

41462

American (AMR)

AF:

0.269

AC:

4115

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.386

AC:

1339

AN:

3470

East Asian (EAS)

AF:

0.427

AC:

2199

AN:

5154

South Asian (SAS)

AF:

0.434

AC:

2089

AN:

4818

European-Finnish (FIN)

AF:

0.452

AC:

4779

AN:

10568

Middle Eastern (MID)

AF:

0.293

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.384

AC:

26103

AN:

67978

Other (OTH)

AF:

0.356

AC:

750

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1832

3663

5495

7326

9158

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

550

1100

1650

2200

2750

<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:

0.367

Hom.:

4634

Bravo

AF:

0.352

Asia WGS

AF:

0.421

AC:

1463

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

7.2

(source)

DANN

Benign

0.51

PhyloP100

0.15

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over