X-77456068-C-T

Variant summary

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

The NM_003868.3(FGF16):​c.379-209C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00522 in 112,337 control chromosomes in the GnomAD database, including 2 homozygotes. There are 169 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0052 ( 2 hom., 169 hem., cov: 23)

Consequence

FGF16
NM_003868.3 intron

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.971
Variant links:
Genes affected
FGF16 (HGNC:3672): (fibroblast growth factor 16) This gene encodes a member of a family of proteins that are involved in a variety of biological processes, including embryonic development, cell growth, morphogenesis, tissue repair, tumor growth and invasion. This gene is expressed in cardiac cells and is required for proper heart development. Mutation in this gene was also observed in individuals with metacarpal 4-5 fusion. [provided by RefSeq, Mar 2014]

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=-0.94).
BP6
Variant X-77456068-C-T is Benign according to our data. Variant chrX-77456068-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1216118.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00522 (586/112337) while in subpopulation AFR AF= 0.0166 (513/30908). AF 95% confidence interval is 0.0154. There are 2 homozygotes in gnomad4. There are 169 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 2 XL gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FGF16NM_003868.3 linkc.379-209C>T intron_variant Intron 2 of 2 ENST00000439435.3 NP_003859.1 O43320A0A7U3L5H2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FGF16ENST00000439435.3 linkc.379-209C>T intron_variant Intron 2 of 2 1 NM_003868.3 ENSP00000399324.2 O43320

Frequencies

GnomAD3 genomes
AF:
0.00517
AC:
581
AN:
112283
Hom.:
2
Cov.:
23
AF XY:
0.00485
AC XY:
167
AN XY:
34445
show subpopulations
Gnomad AFR
AF:
0.0164
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00263
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00370
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000469
Gnomad OTH
AF:
0.00727
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00522
AC:
586
AN:
112337
Hom.:
2
Cov.:
23
AF XY:
0.00490
AC XY:
169
AN XY:
34509
show subpopulations
Gnomad4 AFR
AF:
0.0166
Gnomad4 AMR
AF:
0.00262
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00334
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000469
Gnomad4 OTH
AF:
0.00718
Alfa
AF:
0.00227
Hom.:
12
Bravo
AF:
0.00593

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Jul 10, 2018
GeneDx
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
1.9
DANN
Benign
0.60

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: rs146784489; hg19: chrX-76711559; API