Genetic Variant SLC47A1P1:n.19581638T>C (chr17-19581638-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 0.221 in 152,126 control chromosomes in the GnomAD database, including 3,897 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 0.22 ( 3895 hom., cov: 31)

Exomes 𝑓: 0.21 ( 2 hom. )

Consequence

SLC47A1P1
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.232

Publications

11 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC47A1P1		n.19581638T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000290454	ENST00000420951.1 link	n.272+1303T>C	intron_variant	Intron 2 of 4	5
SLC47A1P1	ENST00000449666.3 link	n.347+1303T>C	intron_variant	Intron 1 of 7	6
ENSG00000290454	ENST00000454535.5 link	n.129+83T>C	intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.221

AC:

33517

AN:

151940

Hom.:

3865

Cov.:

show subpopulations

Gnomad AFR

AF:

0.297

Gnomad AMI

AF:

0.0980

Gnomad AMR

AF:

0.235

Gnomad ASJ

AF:

0.119

Gnomad EAS

AF:

0.282

Gnomad SAS

AF:

0.206

Gnomad FIN

AF:

0.149

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.186

Gnomad OTH

AF:

0.217

GnomAD4 exome

AF:

0.206

AC:

AN:

Hom.:

AF XY:

0.273

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.286

AC:

AN:

Other (OTH)

AF:

0.200

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.455

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:

0.221

AC:

33593

AN:

152058

Hom.:

3895

Cov.:

AF XY:

0.219

AC XY:

16270

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.298

AC:

12359

AN:

41438

American (AMR)

AF:

0.236

AC:

3600

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.119

AC:

411

AN:

3468

East Asian (EAS)

AF:

0.282

AC:

1458

AN:

5170

South Asian (SAS)

AF:

0.205

AC:

988

AN:

4814

European-Finnish (FIN)

AF:

0.149

AC:

1583

AN:

10606

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.186

AC:

12610

AN:

67964

Other (OTH)

AF:

0.217

AC:

458

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1311

2622

3932

5243

6554

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

346

692

1038

1384

1730

<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:

0.200

Hom.:

9355

Bravo

AF:

0.233

Asia WGS

AF:

0.240

AC:

838

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.3

(source)

DANN

Benign

0.41

PhyloP100

-0.23

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