Genetic Variant C14orf28:p.Glu309Asp (chr14-44905544-G-T) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001017923.2(C14orf28):c.927G>T(p.Glu309Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00594 in 1,505,316 control chromosomes in the GnomAD database, including 445 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.030 ( 222 hom., cov: 32)

Exomes 𝑓: 0.0032 ( 223 hom. )

Consequence

C14orf28
NM_001017923.2 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.81

Variant links:

Genes affected

C14orf28 (HGNC:19834): (chromosome 14 open reading frame 28)

C14orf28 links:

ENSG00000258949 (HGNC:):

ENSG00000258949 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0016608238).

BP6

Variant 14-44905544-G-T is Benign according to our data. Variant chr14-44905544-G-T is described in ClinVar as [Benign]. Clinvar id is 789639.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C14orf28	NM_001017923.2 link	c.927G>T	p.Glu309Asp	missense_variant	Exon 5 of 5	ENST00000325192.8	NP_001017923.1	Q4W4Y0
C14orf28	XM_011536408.1 link	c.447G>T	p.Glu149Asp	missense_variant	Exon 4 of 4		XP_011534710.1
LOC101927418	NR_110050.1 link	n.161+6213C>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
C14orf28	ENST00000325192.8 link	c.927G>T	p.Glu309Asp	missense_variant	Exon 5 of 5	1	NM_001017923.2	ENSP00000326846.3	Q4W4Y0
C14orf28	ENST00000557112.1 link	c.837G>T	p.Glu279Asp	missense_variant	Exon 4 of 4	5		ENSP00000451791.1	G3V4G8
C14orf28	ENST00000555826.5 link	n.1786G>T		non_coding_transcript_exon_variant	Exon 3 of 3	2
ENSG00000258949	ENST00000555157.1 link	n.107+6213C>A		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.0303

AC:

4607

AN:

151974

Hom.:

220

Cov.:

show subpopulations

Gnomad AFR

AF:

0.106

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00865

Gnomad ASJ

AF:

0.00289

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000621

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000265

Gnomad OTH

AF:

0.0191

GnomAD3 exomes

AF:

0.00776

AC:

1816

AN:

233896

Hom.:

AF XY:

0.00597

AC XY:

758

AN XY:

127038

show subpopulations

Gnomad AFR exome

AF:

0.106

Gnomad AMR exome

AF:

0.00550

Gnomad ASJ exome

AF:

0.00279

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000366

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000167

Gnomad OTH exome

AF:

0.00357

GnomAD4 exome

AF:

0.00318

AC:

4308

AN:

1353224

Hom.:

223

Cov.:

AF XY:

0.00274

AC XY:

1823

AN XY:

665252

show subpopulations

Gnomad4 AFR exome

AF:

0.109

Gnomad4 AMR exome

AF:

0.00655

Gnomad4 ASJ exome

AF:

0.00200

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000861

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000160

Gnomad4 OTH exome

AF:

0.00688

GnomAD4 genome

AF:

0.0304

AC:

4628

AN:

152092

Hom.:

222

Cov.:

AF XY:

0.0292

AC XY:

2168

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.107

Gnomad4 AMR

AF:

0.00864

Gnomad4 ASJ

AF:

0.00289

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000622

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000265

Gnomad4 OTH

AF:

0.0189

Alfa

AF:

0.00498

Hom.:

Bravo

AF:

0.0339

TwinsUK

AF:

0.000270

AC:

ALSPAC

AF:

0.000259

AC:

ESP6500AA

AF:

0.0947

AC:

417

ESP6500EA

AF:

0.000465

AC:

ExAC

AF:

0.00959

AC:

1164

Asia WGS

AF:

0.00780

AC:

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Dec 31, 2019

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.15

BayesDel_addAF

Benign

-0.68

BayesDel_noAF

Benign

-0.67

CADD

Benign

DANN

Benign

0.94

DEOGEN2

Benign

0.023

T;.

Eigen

Benign

-0.27

Eigen_PC

Benign

-0.066

FATHMM_MKL

Benign

0.73

LIST_S2

Benign

0.69

T;T

MetaRNN

Benign

0.0017

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-0.20

N;.

PROVEAN

Benign

-1.6

N;N

REVEL

Benign

0.076

Sift

Benign

0.14

T;T

Sift4G

Benign

0.44

T;T

Polyphen

0.0010

B;.

Vest4

0.038

MutPred

0.21

Loss of methylation at K310 (P = 0.0601);.;

MVP

0.23

MPC

0.23

ClinPred

0.0099

GERP RS

3.8

Varity_R

0.11

gMVP

0.13

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