Variant 14-44904481-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_001017923.2(C14orf28):c.701C>T(p.Ser234Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00233 in 1,612,046 control chromosomes in the GnomAD database, including 84 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.013 ( 47 hom., cov: 33)

Exomes 𝑓: 0.0012 ( 37 hom. )

Consequence

C14orf28
NM_001017923.2 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.57

Variant links:

Genes affected

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

C14orf28 links:

(HGNC:):

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 (MetaRNN=0.0068749487).

BP6

Variant 14-44904481-C-T is Benign according to our data. Variant chr14-44904481-C-T is described in ClinVar as [Benign]. Clinvar id is 776833.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0128 (1951/152230) while in subpopulation AFR AF= 0.045 (1872/41556). AF 95% confidence interval is 0.0433. There are 47 homozygotes in gnomad4. There are 901 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 47 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
C14orf28	NM_001017923.2 linkuse as main transcript	c.701C>T	p.Ser234Phe	missense_variant	4/5	ENST00000325192.8	NP_001017923.1
LOC101927418	NR_110050.1 linkuse as main transcript	n.162-5168G>A		intron_variant, non_coding_transcript_variant
C14orf28	XM_011536408.1 linkuse as main transcript	c.221C>T	p.Ser74Phe	missense_variant	3/4		XP_011534710.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C14orf28	ENST00000325192.8 linkuse as main transcript	c.701C>T	p.Ser234Phe	missense_variant	4/5	1	NM_001017923.2	ENSP00000326846	P1
	ENST00000555157.1 linkuse as main transcript	n.108-5168G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0128

AC:

1951

AN:

152112

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0452

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00386

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000736

Gnomad OTH

AF:

0.00670

GnomAD3 exomes

AF:

0.00327

AC:

818

AN:

250210

Hom.:

AF XY:

0.00228

AC XY:

308

AN XY:

135252

show subpopulations

Gnomad AFR exome

AF:

0.0460

Gnomad AMR exome

AF:

0.00170

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000329

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000441

Gnomad OTH exome

AF:

0.00148

GnomAD4 exome

AF:

0.00123

AC:

1802

AN:

1459816

Hom.:

Cov.:

AF XY:

0.00102

AC XY:

737

AN XY:

726096

show subpopulations

Gnomad4 AFR exome

AF:

0.0470

Gnomad4 AMR exome

AF:

0.00184

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000350

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000117

Gnomad4 OTH exome

AF:

0.00219

GnomAD4 genome

AF:

0.0128

AC:

1951

AN:

152230

Hom.:

Cov.:

AF XY:

0.0121

AC XY:

901

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.0450

Gnomad4 AMR

AF:

0.00392

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000736

Gnomad4 OTH

AF:

0.00664

Alfa

AF:

0.00232

Hom.:

Bravo

AF:

0.0142

ESP6500AA

AF:

0.0474

AC:

209

ESP6500EA

AF:

0.000349

AC:

ExAC

AF:

0.00425

AC:

516

Asia WGS

AF:

0.00173

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jun 26, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.41

BayesDel_addAF

Benign

-0.50

BayesDel_noAF

Benign

-0.45

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.12

T;.

Eigen

Uncertain

0.26

Eigen_PC

Uncertain

0.36

FATHMM_MKL

Uncertain

0.88

LIST_S2

Benign

0.71

T;T

MetaRNN

Benign

0.0069

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.97

L;.

MutationTaster

Benign

1.0

D;D

PROVEAN

Pathogenic

-5.7

D;D

REVEL

Benign

0.11

Sift

Benign

0.045

D;D

Sift4G

Pathogenic

0.0

D;D

Polyphen

0.83

P;.

Vest4

0.75

MVP

0.39

MPC

0.052

ClinPred

0.047

GERP RS

5.1

Varity_R

0.52

gMVP

0.59

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