10-101770141-TAAAAAAAAAAAAAAA-TAAAAAAAAAAAAAAAAAAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The NM_033163.5(FGF8):​c.*184_*187dupTTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000025 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00037 ( 0 hom. )

Consequence

FGF8
NM_033163.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.108
Variant links:
Genes affected
FGF8 (HGNC:3686): (fibroblast growth factor 8) The protein encoded by this gene is a member of the fibroblast growth factor (FGF) family. FGF family members possess broad mitogenic and cell survival activities, and are involved in a variety of biological processes, including embryonic development, cell growth, morphogenesis, tissue repair, tumor growth and invasion. This protein is known to be a factor that supports androgen and anchorage independent growth of mammary tumor cells. Overexpression of this gene has been shown to increase tumor growth and angiogensis. The adult expression of this gene is restricted to testes and ovaries. Temporal and spatial pattern of this gene expression suggests its function as an embryonic epithelial factor. Studies of the mouse and chick homologs revealed roles in midbrain and limb development, organogenesis, embryo gastrulation and left-right axis determination. The alternative splicing of this gene results in four transcript variants. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BS1
Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.000371 (101/272058) while in subpopulation AFR AF= 0.0008 (6/7498). AF 95% confidence interval is 0.000379. There are 0 homozygotes in gnomad4_exome. There are 54 alleles in male gnomad4_exome subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High AC in GnomAdExome4 at 101 AD,Digenic gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FGF8NM_033163.5 linkc.*184_*187dupTTTT 3_prime_UTR_variant Exon 6 of 6 ENST00000320185.7 NP_149353.1 P55075-4A1A515

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FGF8ENST00000320185 linkc.*184_*187dupTTTT 3_prime_UTR_variant Exon 6 of 6 1 NM_033163.5 ENSP00000321797.2 P55075-4
FGF8ENST00000344255 linkc.*184_*187dupTTTT 3_prime_UTR_variant Exon 6 of 6 1 ENSP00000340039.3 P55075-1
FGF8ENST00000469792.6 linkn.*883_*886dupTTTT splice_region_variant, non_coding_transcript_exon_variant Exon 5 of 5 5 ENSP00000473299.1 R4GMQ3
FGF8ENST00000469792.6 linkn.*883_*886dupTTTT 3_prime_UTR_variant Exon 5 of 5 5 ENSP00000473299.1 R4GMQ3

Frequencies

GnomAD3 genomes
AF:
0.0000248
AC:
3
AN:
120776
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000512
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.000371
AC:
101
AN:
272058
Hom.:
0
Cov.:
0
AF XY:
0.000387
AC XY:
54
AN XY:
139688
show subpopulations
Gnomad4 AFR exome
AF:
0.000800
Gnomad4 AMR exome
AF:
0.000409
Gnomad4 ASJ exome
AF:
0.000110
Gnomad4 EAS exome
AF:
0.0000462
Gnomad4 SAS exome
AF:
0.0000661
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000461
Gnomad4 OTH exome
AF:
0.000541
GnomAD4 genome
AF:
0.0000248
AC:
3
AN:
120776
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
57198
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000512
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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: rs11322844; hg19: chr10-103529898; API