Genetic Variant NM_017946.4:c.*672C>T (chr7-30014063-G-A) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_017946.4(FKBP14):c.*672C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 151,832 control chromosomes in the GnomAD database, including 2,598 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.18 ( 2597 hom., cov: 31)

Exomes 𝑓: 0.11 ( 1 hom. )

Consequence

FKBP14
NM_017946.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.886

Variant links:

Genes affected

FKBP14 (HGNC:18625): (FKBP prolyl isomerase 14) The protein encoded by this gene is a member of the FK506-binding protein family of peptidyl-prolyl cis-trans isomerases. The encoded protein is found in the lumen of the endoplasmic reticulum, where it is thought to accelerate protein folding. Defects in this gene are a cause of a type of Ehlers-Danlos syndrome (EDS). Both a protein-coding variant and noncoding variants are transcribed from this gene. [provided by RefSeq, Mar 2012]

FKBP14 links:

FKBP14-AS1 (HGNC:40990): (FKBP14 antisense RNA 1)

FKBP14-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BP6

Variant 7-30014063-G-A is Benign according to our data. Variant chr7-30014063-G-A is described in ClinVar as [Benign]. Clinvar id is 402867.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FKBP14	NM_017946.4 link	c.*672C>T		3_prime_UTR_variant	Exon 4 of 4	ENST00000222803.10	NP_060416.1	Q9NWM8A0A090N7V8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
FKBP14	ENST00000222803 link	c.*672C>T	3_prime_UTR_variant	Exon 4 of 4	1	NM_017946.4	ENSP00000222803.5	Q9NWM8
FKBP14-AS1	ENST00000419103.1 link	n.344+5686G>A	intron_variant	Intron 2 of 2	4
FKBP14-AS1	ENST00000422239.6 link	n.679+5686G>A	intron_variant	Intron 3 of 3	5
FKBP14	ENST00000419018.1 link	n.*955C>T	downstream_gene_variant		1		ENSP00000406270.1	F8WBZ0

Frequencies

GnomAD3 genomes

AF:

0.180

AC:

27298

AN:

151686

Hom.:

2585

Cov.:

show subpopulations

Gnomad AFR

AF:

0.240

Gnomad AMI

AF:

0.169

Gnomad AMR

AF:

0.170

Gnomad ASJ

AF:

0.208

Gnomad EAS

AF:

0.0747

Gnomad SAS

AF:

0.140

Gnomad FIN

AF:

0.149

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.160

Gnomad OTH

AF:

0.178

GnomAD4 exome

AF:

0.107

AC:

AN:

Hom.:

Cov.:

AF XY:

0.107

AC XY:

AN XY:

show subpopulations

Gnomad4 NFE exome

AF:

0.115

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.180

AC:

27335

AN:

151804

Hom.:

2597

Cov.:

AF XY:

0.178

AC XY:

13208

AN XY:

74172

show subpopulations

Gnomad4 AFR

AF:

0.241

Gnomad4 AMR

AF:

0.169

Gnomad4 ASJ

AF:

0.208

Gnomad4 EAS

AF:

0.0748

Gnomad4 SAS

AF:

0.139

Gnomad4 FIN

AF:

0.149

Gnomad4 NFE

AF:

0.160

Gnomad4 OTH

AF:

0.177

Alfa

AF:

0.0800

Hom.:

Bravo

AF:

0.184

Asia WGS

AF:

0.112

AC:

392

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.92

DANN

Benign

0.46

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over