rs780176806

Variant names:

• chr17-7442615-C-A
• rs780176806
• NM_004112.4:c.430C>A

Your query was ambiguous. Multiple possible variants found:

• chr17-7442615-C-A
• chr17-7442615-C-G
• chr17-7442615-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_004112.4(FGF11):​c.430C>A​(p.Arg144Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: FGF11 NM_004112.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.88

Genes affected

FGF11 (HGNC:3667): (fibroblast growth factor 11) 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. The function of this gene has not yet been determined. The expression pattern of the mouse homolog implies a role in nervous system development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]

ENSG00000272884 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FGF11	NM_004112.4	c.430C>A	p.Arg144Ser	missense_variant	Exon 4 of 5	ENST00000293829.9	NP_004103.1
FGF11	NM_001303460.2	c.253C>A	p.Arg85Ser	missense_variant	Exon 4 of 5		NP_001290389.1
FGF11	NR_130156.2	n.470C>A		non_coding_transcript_exon_variant	Exon 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FGF11	ENST00000293829.9	c.430C>A	p.Arg144Ser	missense_variant	Exon 4 of 5	1	NM_004112.4	ENSP00000293829.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1461842 Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0 AN XY: 727226

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Alfa AF: 0.0000329 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.73
BayesDel_addAF	Benign	0.0032	T
BayesDel_noAF	Benign	-0.23
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.52	.;D;.;.;.
Eigen	Uncertain	0.29
Eigen_PC	Uncertain	0.39
FATHMM_MKL	Uncertain	0.86	D
M_CAP	Benign	0.020	T
MetaRNN	Uncertain	0.53	D;D;D;D;D
MetaSVM	Benign	-0.59	T
MutationAssessor	Benign	1.5	.;L;.;.;.
PrimateAI	Uncertain	0.68	T
PROVEAN	Benign	-1.5	.;N;.;.;.
REVEL	Benign	0.13
Sift	Uncertain	0.020	.;D;.;.;.
Sift4G	Uncertain	0.0030	D;D;D;D;D
Polyphen		0.71	.;P;.;.;.
Vest4		0.38
MVP		0.81
MPC		0.32
ClinPred		0.92	D
GERP RS		5.0
Varity_R		0.64
gMVP		0.46

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

Other links and lift over

dbSNP: rs780176806; hg19: chr17-7345934;