dbSNP rs169494: FKBPL:c.-79C>T (chr6-32130099-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_022110.4(FKBPL):c.-79C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 500,408 control chromosomes in the GnomAD database, including 4,705 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 0.10 ( 1009 hom., cov: 31)

Exomes 𝑓: 0.11 ( 3696 hom. )

Consequence

FKBPL
NM_022110.4 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.443

Publications

25 publications found

Variant links:

Genes affected

FKBPL (HGNC:13949): (FKBP prolyl isomerase like) The protein encoded by this gene has similarity to the immunophilin protein family, which play a role in immunoregulation and basic cellular processes involving protein folding and trafficking. The encoded protein is thought to have a potential role in the induced radioresistance. Also it appears to have some involvement in the control of the cell cycle. [provided by RefSeq, Jul 2008]

FKBPL 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=-0.85).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FKBPL	NM_022110.4 link	c.-79C>T		5_prime_UTR_variant	Exon 1 of 2	ENST00000375156.4	NP_071393.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FKBPL	ENST00000375156.4 link	c.-79C>T		5_prime_UTR_variant	Exon 1 of 2	1	NM_022110.4	ENSP00000364298.3

Frequencies

GnomAD3 genomes

AF:

0.102

AC:

15491

AN:

152014

Hom.:

1004

Cov.:

show subpopulations

Gnomad AFR

AF:

0.133

Gnomad AMI

AF:

0.0165

Gnomad AMR

AF:

0.101

Gnomad ASJ

AF:

0.0717

Gnomad EAS

AF:

0.103

Gnomad SAS

AF:

0.294

Gnomad FIN

AF:

0.0605

Gnomad MID

AF:

0.218

Gnomad NFE

AF:

0.0771

Gnomad OTH

AF:

0.135

GnomAD4 exome

AF:

0.113

AC:

39492

AN:

348276

Hom.:

3696

Cov.:

AF XY:

0.128

AC XY:

23817

AN XY:

185592

show subpopulations

African (AFR)

AF:

0.131

AC:

1350

AN:

10292

American (AMR)

AF:

0.0883

AC:

1204

AN:

13640

Ashkenazi Jewish (ASJ)

AF:

0.0688

AC:

743

AN:

10806

East Asian (EAS)

AF:

0.106

AC:

2303

AN:

21786

South Asian (SAS)

AF:

0.336

AC:

13665

AN:

40666

European-Finnish (FIN)

AF:

0.0691

AC:

1226

AN:

17736

Middle Eastern (MID)

AF:

0.183

AC:

283

AN:

1544

European-Non Finnish (NFE)

AF:

0.0785

AC:

16638

AN:

211814

Other (OTH)

AF:

0.104

AC:

2080

AN:

19992

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.521

Heterozygous variant carriers

1590

3181

4771

6362

7952

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

192

384

576

768

960

<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:

0.102

AC:

15515

AN:

152132

Hom.:

1009

Cov.:

AF XY:

0.107

AC XY:

7936

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.134

AC:

5538

AN:

41482

American (AMR)

AF:

0.101

AC:

1544

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0717

AC:

249

AN:

3472

East Asian (EAS)

AF:

0.103

AC:

531

AN:

5166

South Asian (SAS)

AF:

0.293

AC:

1411

AN:

4814

European-Finnish (FIN)

AF:

0.0605

AC:

641

AN:

10592

Middle Eastern (MID)

AF:

0.201

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0771

AC:

5246

AN:

68006

Other (OTH)

AF:

0.133

AC:

281

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

687

1374

2060

2747

3434

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

188

376

564

752

940

<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:

0.0857

Hom.:

2336

Bravo

AF:

0.101

Asia WGS

AF:

0.228

AC:

796

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

(source)

DANN

Benign

0.69

PhyloP100

0.44

PromoterAI

-0.024

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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