Genetic Variant S1PR1-DT:n.284G>C (chr1-101236367-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000432195.3(S1PR1-DT):n.284G>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 0.37 in 152,190 control chromosomes in the GnomAD database, including 10,822 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 ( 10801 hom., cov: 30)

Exomes 𝑓: 0.32 ( 21 hom. )

Consequence

S1PR1-DT
ENST00000432195.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.99

Publications

6 publications found

Variant links:

Genes affected

S1PR1-DT (HGNC:55842): (S1PR1 divergent transcript)

S1PR1-DT 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=-0.69).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
S1PR1-DT	NR_104626.1 link	n.162G>C		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
S1PR1-DT	ENST00000432195.3 link	n.284G>C	non_coding_transcript_exon_variant	Exon 1 of 2	2
S1PR1-DT	ENST00000686331.3 link	n.449G>C	non_coding_transcript_exon_variant	Exon 1 of 1
S1PR1-DT	ENST00000820226.1 link	n.258G>C	non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.370

AC:

56103

AN:

151686

Hom.:

10797

Cov.:

show subpopulations

Gnomad AFR

AF:

0.419

Gnomad AMI

AF:

0.362

Gnomad AMR

AF:

0.300

Gnomad ASJ

AF:

0.329

Gnomad EAS

AF:

0.118

Gnomad SAS

AF:

0.414

Gnomad FIN

AF:

0.373

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.374

Gnomad OTH

AF:

0.355

GnomAD4 exome

AF:

0.318

AC:

122

AN:

384

Hom.:

Cov.:

AF XY:

0.316

AC XY:

AN XY:

294

show subpopulations

African (AFR)

AF:

0.200

AC:

AN:

American (AMR)

AF:

0.250

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.0556

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.438

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.340

AC:

106

AN:

312

Other (OTH)

AF:

0.0833

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.370

AC:

56122

AN:

151806

Hom.:

10801

Cov.:

AF XY:

0.366

AC XY:

27160

AN XY:

74188

show subpopulations

African (AFR)

AF:

0.418

AC:

17291

AN:

41360

American (AMR)

AF:

0.299

AC:

4566

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.329

AC:

1142

AN:

3472

East Asian (EAS)

AF:

0.117

AC:

605

AN:

5152

South Asian (SAS)

AF:

0.415

AC:

1999

AN:

4816

European-Finnish (FIN)

AF:

0.373

AC:

3927

AN:

10538

Middle Eastern (MID)

AF:

0.323

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.374

AC:

25427

AN:

67902

Other (OTH)

AF:

0.351

AC:

741

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1768

3537

5305

7074

8842

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

546

1092

1638

2184

2730

<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:

0.260

Hom.:

649

Bravo

AF:

0.361

Asia WGS

AF:

0.290

AC:

1009

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

1.6

(source)

DANN

Benign

0.84

PhyloP100

-4.0

PromoterAI

-0.045

Neutral

(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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over