Genetic Variant ENST00000575331.1:n.3310A>C (chr17-7443723-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000575331.1(ENSG00000272884):n.3310A>C 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 0.686 in 152,206 control chromosomes in the GnomAD database, including 36,586 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 0.69 ( 36540 hom., cov: 32)

Exomes 𝑓: 0.80 ( 46 hom. )

Consequence

ENSG00000272884
ENST00000575331.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.411

Publications

16 publications found

Variant links:

Genes affected

ENSG00000272884 (HGNC:):

ENSG00000272884 links:

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]

FGF11 links:

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=-0.94).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
FGF11	NM_004112.4 link	c.*577A>C	3_prime_UTR_variant	Exon 5 of 5	ENST00000293829.9	NP_004103.1	Q92914A0A7U3JVZ5
FGF11	NR_130156.2 link	n.1295A>C	non_coding_transcript_exon_variant	Exon 5 of 5
FGF11	NM_001303460.2 link	c.*577A>C	3_prime_UTR_variant	Exon 5 of 5		NP_001290389.1	Q92914B7Z1C3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FGF11	ENST00000293829.9 link	c.*577A>C		3_prime_UTR_variant	Exon 5 of 5	1	NM_004112.4	ENSP00000293829.4		Q92914

Frequencies

GnomAD3 genomes

AF:

0.686

AC:

104301

AN:

151944

Hom.:

36526

Cov.:

show subpopulations

Gnomad AFR

AF:

0.710

Gnomad AMI

AF:

0.820

Gnomad AMR

AF:

0.616

Gnomad ASJ

AF:

0.681

Gnomad EAS

AF:

0.231

Gnomad SAS

AF:

0.615

Gnomad FIN

AF:

0.688

Gnomad MID

AF:

0.703

Gnomad NFE

AF:

0.726

Gnomad OTH

AF:

0.697

GnomAD4 exome

AF:

0.796

AC:

113

AN:

142

Hom.:

Cov.:

AF XY:

0.829

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

0.750

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.833

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.798

AC:

AN:

114

Other (OTH)

AF:

0.700

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.532

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.686

AC:

104362

AN:

152064

Hom.:

36540

Cov.:

AF XY:

0.679

AC XY:

50442

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.709

AC:

29400

AN:

41470

American (AMR)

AF:

0.616

AC:

9418

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.681

AC:

2363

AN:

3470

East Asian (EAS)

AF:

0.231

AC:

1192

AN:

5162

South Asian (SAS)

AF:

0.615

AC:

2961

AN:

4816

European-Finnish (FIN)

AF:

0.688

AC:

7271

AN:

10570

Middle Eastern (MID)

AF:

0.711

AC:

209

AN:

294

European-Non Finnish (NFE)

AF:

0.726

AC:

49325

AN:

67976

Other (OTH)

AF:

0.698

AC:

1475

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1634

3267

4901

6534

8168

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

808

1616

2424

3232

4040

<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:

0.713

Hom.:

50448

Bravo

AF:

0.680

Asia WGS

AF:

0.494

AC:

1719

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

6.6

(source)

DANN

Benign

0.46

PhyloP100

0.41

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over