Genetic Variant ENST00000686331.3:n.891A>G (chr1-101235925-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 ENST00000686331.3(S1PR1-DT):n.891A>G 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 0.342 in 151,808 control chromosomes in the GnomAD database, including 9,293 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 0.34 ( 9293 hom., cov: 30)

Exomes 𝑓: 0.28 ( 0 hom. )

Consequence

S1PR1-DT
ENST00000686331.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.230

Publications

2 publications found

Variant links:

Genes affected

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

S1PR1-DT links:

ENSG00000306729 (HGNC:):

ENSG00000306729 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=-0.82).

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.205-44A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
S1PR1-DT	ENST00000686331.3 link	n.891A>G	non_coding_transcript_exon_variant	Exon 1 of 1
S1PR1-DT	ENST00000820226.1 link	n.700A>G	non_coding_transcript_exon_variant	Exon 1 of 2
S1PR1-DT	ENST00000820227.1 link	n.689A>G	non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.342

AC:

51812

AN:

151672

Hom.:

9286

Cov.:

show subpopulations

Gnomad AFR

AF:

0.418

Gnomad AMI

AF:

0.351

Gnomad AMR

AF:

0.263

Gnomad ASJ

AF:

0.262

Gnomad EAS

AF:

0.127

Gnomad SAS

AF:

0.415

Gnomad FIN

AF:

0.346

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.328

Gnomad OTH

AF:

0.318

GnomAD4 exome

AF:

0.278

AC:

AN:

Hom.:

Cov.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.250

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

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:

0.342

AC:

51839

AN:

151790

Hom.:

9293

Cov.:

AF XY:

0.339

AC XY:

25181

AN XY:

74186

show subpopulations

African (AFR)

AF:

0.418

AC:

17272

AN:

41326

American (AMR)

AF:

0.263

AC:

4015

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.262

AC:

908

AN:

3472

East Asian (EAS)

AF:

0.127

AC:

655

AN:

5168

South Asian (SAS)

AF:

0.416

AC:

2001

AN:

4812

European-Finnish (FIN)

AF:

0.346

AC:

3639

AN:

10528

Middle Eastern (MID)

AF:

0.286

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.328

AC:

22285

AN:

67914

Other (OTH)

AF:

0.314

AC:

662

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1690

3381

5071

6762

8452

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

508

1016

1524

2032

2540

<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:

0.330

Hom.:

7834

Bravo

AF:

0.332

Asia WGS

AF:

0.288

AC:

1000

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

8.1

(source)

DANN

Benign

0.52

PhyloP100

0.23

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