X-77454272-GTTTTTTTTTTTTTTTTTTTTT-GTTTT

Variant names:

• chrX-77454272-GTTTTTTTTTTTTTTTTT-G
• rs782034788
• NM_003868.3:c.378+26_378+42delTTTTTTTTTTTTTTTTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_003868.3(FGF16):​c.378+26_378+42delTTTTTTTTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.000044 (0 hom., 0 hem., cov: 11)
• Consequence: FGF16 NM_003868.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89
• Publications: 0 publications found

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]

FGF16 Gene-Disease associations (from GenCC):

• syndactyly type 8

  Inheritance: AD, XL Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)

ENSG00000295984 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003868.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FGF16	NM_003868.3	MANE Select	c.378+26_378+42delTTTTTTTTTTTTTTTTT		intron	N/A	NP_003859.1	O43320

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FGF16	ENST00000439435.3	TSL:1 MANE Select	c.378+13_378+29delTTTTTTTTTTTTTTTTT		intron	N/A	ENSP00000399324.2	O43320
	ENSG00000295984	ENST00000734738.1		n.179+6917_179+6933delAAAAAAAAAAAAAAAAA		intron	N/A
	ENSG00000295984	ENST00000734739.1		n.45+6917_45+6933delAAAAAAAAAAAAAAAAA		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0000436 AC: 2 AN: 45911 Hom.: 0 Cov.: 11

Gnomad AFR AF: 0.000201

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: 0.00

Gnomad OTH AF: 0.00

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0000436 AC: 2 AN: 45906 Hom.: 0 Cov.: 11 AF XY: 0.00 AC XY: 0 AN XY: 9102

African (AFR) AF: 0.000201 AC: 2 AN: 9955

American (AMR) AF: 0.00 AC: 0 AN: 3654

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1428

East Asian (EAS) AF: 0.00 AC: 0 AN: 1198

South Asian (SAS) AF: 0.00 AC: 0 AN: 545

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1179

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 58

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 26952

Other (OTH) AF: 0.00 AC: 0 AN: 571

Alfa AF: 0.00 Hom.: 186

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs782034788; hg19: chrX-76709763;