dbSNP rs2120273: SLC47A1P1:n.19582422T>C (chr17-19582422-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The variant allele was found at a frequency of 0.194 in 151,696 control chromosomes in the GnomAD database, including 2,675 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 0.19 ( 2672 hom., cov: 32)

Exomes 𝑓: 0.23 ( 3 hom. )

Consequence

SLC47A1P1
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.252

Publications

3 publications found

Variant links:

Genes affected

SLC47A1P1 (HGNC:51849): (SLC47A1 pseudogene 1)

SLC47A1P1 links:

ENSG00000290454 (HGNC:):

ENSG00000290454 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC47A1P1		n.19582422T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000290454	ENST00000420951.1 link	n.272+2087T>C	intron_variant	Intron 2 of 4	5
SLC47A1P1	ENST00000449666.3 link	n.347+2087T>C	intron_variant	Intron 1 of 7	6
ENSG00000290454	ENST00000454535.5 link	n.129+867T>C	intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.194

AC:

29372

AN:

151482

Hom.:

2667

Cov.:

show subpopulations

Gnomad AFR

AF:

0.181

Gnomad AMI

AF:

0.116

Gnomad AMR

AF:

0.230

Gnomad ASJ

AF:

0.122

Gnomad EAS

AF:

0.235

Gnomad SAS

AF:

0.183

Gnomad FIN

AF:

0.169

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.200

Gnomad OTH

AF:

0.197

GnomAD4 exome

AF:

0.228

AC:

AN:

Hom.:

AF XY:

0.171

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.333

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.194

AC:

AN:

Other (OTH)

AF:

0.400

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.412

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:

0.194

AC:

29401

AN:

151604

Hom.:

2672

Cov.:

AF XY:

0.191

AC XY:

14186

AN XY:

74120

show subpopulations

African (AFR)

AF:

0.181

AC:

7506

AN:

41412

American (AMR)

AF:

0.231

AC:

3522

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.122

AC:

422

AN:

3458

East Asian (EAS)

AF:

0.234

AC:

1198

AN:

5112

South Asian (SAS)

AF:

0.183

AC:

873

AN:

4782

European-Finnish (FIN)

AF:

0.169

AC:

1777

AN:

10524

Middle Eastern (MID)

AF:

0.122

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.200

AC:

13548

AN:

67758

Other (OTH)

AF:

0.197

AC:

413

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

1223

2446

3668

4891

6114

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

312

624

936

1248

1560

<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:

0.197

Hom.:

330

Asia WGS

AF:

0.210

AC:

734

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.1

(source)

DANN

Benign

0.82

PhyloP100

-0.25

Mutation Taster

=100/0

polymorphism

(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