8-120162495-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_021110.4(COL14A1):ā€‹c.275A>Gā€‹(p.Asp92Gly) variant causes a missense change. The variant allele was found at a frequency of 0.000996 in 1,613,182 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā˜…).

Frequency

Genomes: š‘“ 0.00056 ( 3 hom., cov: 33)
Exomes š‘“: 0.0010 ( 22 hom. )

Consequence

COL14A1
NM_021110.4 missense

Scores

4
14

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 6.35
Variant links:
Genes affected
COL14A1 (HGNC:2191): (collagen type XIV alpha 1 chain) This gene encodes the alpha chain of type XIV collagen, a member of the FACIT (fibril-associated collagens with interrupted triple helices) collagen family. Type XIV collagen interacts with the fibril surface and is involved in the regulation of fibrillogenesis. [provided by RefSeq, Jan 2013]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.00811559).
BP6
Variant 8-120162495-A-G is Benign according to our data. Variant chr8-120162495-A-G is described in ClinVar as [Benign]. Clinvar id is 723311.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 3 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
COL14A1NM_021110.4 linkc.275A>G p.Asp92Gly missense_variant 4/48 ENST00000297848.8 NP_066933.1 Q05707-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
COL14A1ENST00000297848.8 linkc.275A>G p.Asp92Gly missense_variant 4/485 NM_021110.4 ENSP00000297848.3 Q05707-1

Frequencies

GnomAD3 genomes
AF:
0.000565
AC:
86
AN:
152236
Hom.:
3
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000262
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.0149
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000103
Gnomad OTH
AF:
0.000478
GnomAD3 exomes
AF:
0.00207
AC:
518
AN:
250100
Hom.:
7
AF XY:
0.00278
AC XY:
376
AN XY:
135188
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000117
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0163
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000132
Gnomad OTH exome
AF:
0.000986
GnomAD4 exome
AF:
0.00104
AC:
1520
AN:
1460828
Hom.:
22
Cov.:
30
AF XY:
0.00150
AC XY:
1093
AN XY:
726648
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.000112
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0155
Gnomad4 FIN exome
AF:
0.0000187
Gnomad4 NFE exome
AF:
0.0000828
Gnomad4 OTH exome
AF:
0.00123
GnomAD4 genome
AF:
0.000564
AC:
86
AN:
152354
Hom.:
3
Cov.:
33
AF XY:
0.000886
AC XY:
66
AN XY:
74498
show subpopulations
Gnomad4 AFR
AF:
0.0000240
Gnomad4 AMR
AF:
0.000261
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.0149
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000103
Gnomad4 OTH
AF:
0.000473
Alfa
AF:
0.000178
Hom.:
0
Bravo
AF:
0.000227
TwinsUK
AF:
0.00
AC:
0
ALSPAC
AF:
0.000259
AC:
1
ExAC
AF:
0.00244
AC:
296
Asia WGS
AF:
0.00606
AC:
21
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 submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpMay 17, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.14
BayesDel_addAF
Benign
-0.42
T
BayesDel_noAF
Benign
-0.37
CADD
Uncertain
24
DANN
Benign
0.48
DEOGEN2
Benign
0.076
.;.;T
Eigen
Uncertain
0.19
Eigen_PC
Uncertain
0.33
FATHMM_MKL
Uncertain
0.96
D
LIST_S2
Uncertain
0.90
D;D;D
MetaRNN
Benign
0.0081
T;T;T
MetaSVM
Benign
-0.97
T
MutationAssessor
Benign
0.75
.;N;N
PrimateAI
Benign
0.45
T
PROVEAN
Benign
-0.37
N;N;N
REVEL
Benign
0.17
Sift
Benign
0.69
T;T;T
Sift4G
Benign
0.26
T;T;T
Polyphen
0.58
.;.;P
Vest4
0.39
MVP
0.43
MPC
0.46
ClinPred
0.052
T
GERP RS
5.6
Varity_R
0.17
gMVP
0.44

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.

Other links and lift over

dbSNP: rs554596714; hg19: chr8-121174734; API