6-31377819-G-A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000449999.1(FGFR3P1):​n.401G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 157,518 control chromosomes in the GnomAD database, including 5,023 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.23 ( 4980 hom., cov: 32)
Exomes 𝑓: 0.12 ( 43 hom. )

Consequence

FGFR3P1
ENST00000449999.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.221

Publications

14 publications found
Variant links:
Genes affected
FGFR3P1 (HGNC:21664): (fibroblast growth factor receptor 3 pseudogene 1)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FGFR3P1 n.31377819G>A intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FGFR3P1ENST00000449999.1 linkn.401G>A non_coding_transcript_exon_variant Exon 1 of 1 6
ENSG00000298426ENST00000755446.1 linkn.327-4161G>A intron_variant Intron 1 of 1
ENSG00000298474ENST00000755731.1 linkn.303+420C>T intron_variant Intron 1 of 1

Frequencies

GnomAD3 genomes
AF:
0.231
AC:
35096
AN:
151972
Hom.:
4979
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.104
Gnomad AMI
AF:
0.353
Gnomad AMR
AF:
0.142
Gnomad ASJ
AF:
0.127
Gnomad EAS
AF:
0.220
Gnomad SAS
AF:
0.139
Gnomad FIN
AF:
0.287
Gnomad MID
AF:
0.178
Gnomad NFE
AF:
0.332
Gnomad OTH
AF:
0.186
GnomAD4 exome
AF:
0.119
AC:
648
AN:
5428
Hom.:
43
Cov.:
0
AF XY:
0.123
AC XY:
329
AN XY:
2684
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.0417
AC:
1
AN:
24
American (AMR)
AF:
0.00
AC:
0
AN:
4
Ashkenazi Jewish (ASJ)
AF:
0.250
AC:
1
AN:
4
East Asian (EAS)
AF:
0.167
AC:
2
AN:
12
South Asian (SAS)
AF:
0.104
AC:
65
AN:
624
European-Finnish (FIN)
AF:
0.113
AC:
476
AN:
4196
Middle Eastern (MID)
AF:
0.0556
AC:
9
AN:
162
European-Non Finnish (NFE)
AF:
0.256
AC:
87
AN:
340
Other (OTH)
AF:
0.113
AC:
7
AN:
62
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.395
Heterozygous variant carriers
0
28
55
83
110
138
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.231
AC:
35113
AN:
152090
Hom.:
4980
Cov.:
32
AF XY:
0.223
AC XY:
16616
AN XY:
74348
show subpopulations
African (AFR)
AF:
0.104
AC:
4308
AN:
41516
American (AMR)
AF:
0.141
AC:
2164
AN:
15300
Ashkenazi Jewish (ASJ)
AF:
0.127
AC:
439
AN:
3470
East Asian (EAS)
AF:
0.220
AC:
1135
AN:
5164
South Asian (SAS)
AF:
0.140
AC:
673
AN:
4816
European-Finnish (FIN)
AF:
0.287
AC:
3031
AN:
10570
Middle Eastern (MID)
AF:
0.182
AC:
53
AN:
292
European-Non Finnish (NFE)
AF:
0.332
AC:
22585
AN:
67934
Other (OTH)
AF:
0.190
AC:
403
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1307
2614
3921
5228
6535
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
372
744
1116
1488
1860
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.293
Hom.:
17171
Bravo
AF:
0.213
Asia WGS
AF:
0.169
AC:
587
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
13
DANN
Benign
0.61
PhyloP100
0.22

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs2507984; hg19: chr6-31345596; API