dbSNP rs7611945: FBRSL1P1:n.116C>T (chr3-125958671-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000466506.1(FBRSL1P1):n.116C>T 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 0.197 in 590,272 control chromosomes in the GnomAD database, including 13,952 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 0.25 ( 5994 hom., cov: 33)

Exomes 𝑓: 0.18 ( 7958 hom. )

Consequence

FBRSL1P1
ENST00000466506.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.15

Publications

13 publications found

Variant links:

Genes affected

FBRSL1P1 (HGNC:56500): (FBRSL1 pseudogene 1)

FBRSL1P1 links:

ENSG00000291096 (HGNC:):

ENSG00000291096 links:

ALG1L1P (HGNC:33721): (ALG1 like 1, pseudogene) Predicted to enable mannosyltransferase activity. Predicted to be involved in protein glycosylation. Predicted to be active in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ALG1L1P links:

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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=-0.79).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
FBRSL1P1		n.125958671C>T	intragenic_variant
ALG1L1P	NR_171196.1 link	n.117-24975G>A	intron_variant	Intron 1 of 5
ALG1L1P	NR_171197.1 link	n.117-24975G>A	intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
FBRSL1P1	ENST00000466506.1 link	n.116C>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000291096	ENST00000774414.1 link	n.206G>A	non_coding_transcript_exon_variant	Exon 1 of 6
ENSG00000291096	ENST00000774415.1 link	n.176G>A	non_coding_transcript_exon_variant	Exon 1 of 7

Frequencies

GnomAD3 genomes

AF:

0.249

AC:

37882

AN:

152032

Hom.:

5986

Cov.:

show subpopulations

Gnomad AFR

AF:

0.447

Gnomad AMI

AF:

0.202

Gnomad AMR

AF:

0.199

Gnomad ASJ

AF:

0.273

Gnomad EAS

AF:

0.0672

Gnomad SAS

AF:

0.129

Gnomad FIN

AF:

0.102

Gnomad MID

AF:

0.275

Gnomad NFE

AF:

0.184

Gnomad OTH

AF:

0.268

GnomAD4 exome

AF:

0.179

AC:

78526

AN:

438122

Hom.:

7958

Cov.:

AF XY:

0.176

AC XY:

41778

AN XY:

237350

show subpopulations

African (AFR)

AF:

0.443

AC:

4020

AN:

9076

American (AMR)

AF:

0.149

AC:

2508

AN:

16886

Ashkenazi Jewish (ASJ)

AF:

0.270

AC:

3616

AN:

13392

East Asian (EAS)

AF:

0.0948

AC:

2362

AN:

24918

South Asian (SAS)

AF:

0.122

AC:

5460

AN:

44882

European-Finnish (FIN)

AF:

0.125

AC:

3932

AN:

31344

Middle Eastern (MID)

AF:

0.247

AC:

795

AN:

3224

European-Non Finnish (NFE)

AF:

0.188

AC:

50518

AN:

269052

Other (OTH)

AF:

0.210

AC:

5315

AN:

25348

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

3186

6372

9558

12744

15930

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

222

444

666

888

1110

<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:

0.249

AC:

37915

AN:

152150

Hom.:

5994

Cov.:

AF XY:

0.242

AC XY:

17981

AN XY:

74398

show subpopulations

African (AFR)

AF:

0.447

AC:

18526

AN:

41478

American (AMR)

AF:

0.199

AC:

3045

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.273

AC:

948

AN:

3470

East Asian (EAS)

AF:

0.0668

AC:

345

AN:

5166

South Asian (SAS)

AF:

0.128

AC:

619

AN:

4824

European-Finnish (FIN)

AF:

0.102

AC:

1081

AN:

10612

Middle Eastern (MID)

AF:

0.279

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.184

AC:

12519

AN:

67976

Other (OTH)

AF:

0.268

AC:

567

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1397

2794

4190

5587

6984

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

362

724

1086

1448

1810

<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:

0.207

Hom.:

14174

Bravo

AF:

0.264

Asia WGS

AF:

0.139

AC:

481

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

7.0

(source)

DANN

Benign

0.80

PhyloP100

-1.1

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