Genetic Variant NM_018242.3:c.87C>T (chr17-19534026-C-T) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BS1BS2

The NM_018242.3(SLC47A1):c.87C>T(p.Ser29Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0122 in 1,547,452 control chromosomes in the GnomAD database, including 172 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 0.0096 ( 11 hom., cov: 32)

Exomes 𝑓: 0.013 ( 161 hom. )

Consequence

SLC47A1
NM_018242.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.21

Publications

6 publications found

Variant links:

Genes affected

SLC47A1 (HGNC:25588): (solute carrier family 47 member 1) This gene is located within the Smith-Magenis syndrome region on chromosome 17. It encodes a protein of unknown function. [provided by RefSeq, Jul 2008]

SLC47A1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.57).

BP7

Synonymous conserved (PhyloP=-1.21 with no splicing effect.

BS1

Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.00964 (1469/152328) while in subpopulation SAS AF = 0.0234 (113/4832). AF 95% confidence interval is 0.0199. There are 11 homozygotes in GnomAd4. There are 709 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 11 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018242.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC47A1	NM_018242.3	MANE Select	c.87C>T	p.Ser29Ser	synonymous	Exon 1 of 17	NP_060712.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
SLC47A1	ENST00000270570.8	TSL:1 MANE Select	c.87C>T	p.Ser29Ser	synonymous	Exon 1 of 17	ENSP00000270570.4
SLC47A1	ENST00000395585.5	TSL:1	c.87C>T	p.Ser29Ser	synonymous	Exon 1 of 19	ENSP00000378951.1
SLC47A1	ENST00000575023.5	TSL:1	c.87C>T	p.Ser29Ser	synonymous	Exon 1 of 7	ENSP00000460164.1

Frequencies

GnomAD3 genomes

AF:

0.00966

AC:

1470

AN:

152212

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00256

Gnomad AMI

AF:

0.0581

Gnomad AMR

AF:

0.0112

Gnomad ASJ

AF:

0.0222

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0236

Gnomad FIN

AF:

0.00518

Gnomad MID

AF:

0.0350

Gnomad NFE

AF:

0.0125

Gnomad OTH

AF:

0.0143

GnomAD2 exomes

AF:

0.0131

AC:

1924

AN:

146932

AF XY:

0.0148

show subpopulations

Gnomad AFR exome

AF:

0.00192

Gnomad AMR exome

AF:

0.00767

Gnomad ASJ exome

AF:

0.0262

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00412

Gnomad NFE exome

AF:

0.0146

Gnomad OTH exome

AF:

0.0155

GnomAD4 exome

AF:

0.0125

AC:

17472

AN:

1395124

Hom.:

161

Cov.:

AF XY:

0.0133

AC XY:

9149

AN XY:

688936

show subpopulations

African (AFR)

AF:

0.00264

AC:

AN:

30694

American (AMR)

AF:

0.00872

AC:

312

AN:

35792

Ashkenazi Jewish (ASJ)

AF:

0.0244

AC:

608

AN:

24950

East Asian (EAS)

AF:

0.000112

AC:

AN:

35574

South Asian (SAS)

AF:

0.0257

AC:

2001

AN:

77996

European-Finnish (FIN)

AF:

0.00476

AC:

228

AN:

47876

Middle Eastern (MID)

AF:

0.0274

AC:

134

AN:

4896

European-Non Finnish (NFE)

AF:

0.0124

AC:

13357

AN:

1079492

Other (OTH)

AF:

0.0129

AC:

747

AN:

57854

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.471

Heterozygous variant carriers

919

1839

2758

3678

4597

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

496

992

1488

1984

2480

<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:

0.00964

AC:

1469

AN:

152328

Hom.:

Cov.:

AF XY:

0.00952

AC XY:

709

AN XY:

74496

show subpopulations

African (AFR)

AF:

0.00255

AC:

106

AN:

41594

American (AMR)

AF:

0.0112

AC:

172

AN:

15310

Ashkenazi Jewish (ASJ)

AF:

0.0222

AC:

AN:

3470

East Asian (EAS)

AF:

0.000193

AC:

AN:

5168

South Asian (SAS)

AF:

0.0234

AC:

113

AN:

4832

European-Finnish (FIN)

AF:

0.00518

AC:

AN:

10628

Middle Eastern (MID)

AF:

0.0342

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0125

AC:

852

AN:

68008

Other (OTH)

AF:

0.0142

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

166

250

333

416

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<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:

0.0128

Hom.:

Bravo

AF:

0.00984

Asia WGS

AF:

0.00867

AC:

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

7.9

(source)

DANN

Benign

0.92

PhyloP100

-1.2

PromoterAI

0.040

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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