Variant chr17-7442647-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2

The ENST00000293829.9(FGF11):c.462C>T(p.Tyr154=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00774 in 1,614,198 control chromosomes in the GnomAD database, including 75 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0055 ( 10 hom., cov: 32)

Exomes 𝑓: 0.0080 ( 65 hom. )

Consequence

FGF11
ENST00000293829.9 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.233

Variant links:

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]

FGF11 links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP6

Variant 17-7442647-C-T is Benign according to our data. Variant chr17-7442647-C-T is described in ClinVar as [Benign]. Clinvar id is 771204.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High AC in GnomAd4 at 837 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
FGF11	NM_004112.4 linkuse as main transcript	c.462C>T	p.Tyr154=	synonymous_variant	4/5	ENST00000293829.9	NP_004103.1
FGF11	NM_001303460.2 linkuse as main transcript	c.285C>T	p.Tyr95=	synonymous_variant	4/5		NP_001290389.1
FGF11	NR_130156.2 linkuse as main transcript	n.502C>T		non_coding_transcript_exon_variant	4/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGF11	ENST00000293829.9 linkuse as main transcript	c.462C>T	p.Tyr154=	synonymous_variant	4/5	1	NM_004112.4	ENSP00000293829	P1
	ENST00000576615.1 linkuse as main transcript	n.69+612G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.00551

AC:

838

AN:

152204

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00116

Gnomad AMI

AF:

0.0274

Gnomad AMR

AF:

0.00458

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00766

Gnomad FIN

AF:

0.00207

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.00901

Gnomad OTH

AF:

0.00382

GnomAD3 exomes

AF:

0.00606

AC:

1525

AN:

251494

Hom.:

AF XY:

0.00648

AC XY:

881

AN XY:

135922

show subpopulations

Gnomad AFR exome

AF:

0.00111

Gnomad AMR exome

AF:

0.00341

Gnomad ASJ exome

AF:

0.00377

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.00650

Gnomad FIN exome

AF:

0.00203

Gnomad NFE exome

AF:

0.00943

Gnomad OTH exome

AF:

0.00537

GnomAD4 exome

AF:

0.00797

AC:

11650

AN:

1461876

Hom.:

Cov.:

AF XY:

0.00791

AC XY:

5751

AN XY:

727242

show subpopulations

Gnomad4 AFR exome

AF:

0.00122

Gnomad4 AMR exome

AF:

0.00331

Gnomad4 ASJ exome

AF:

0.00337

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00715

Gnomad4 FIN exome

AF:

0.00204

Gnomad4 NFE exome

AF:

0.00914

Gnomad4 OTH exome

AF:

0.00712

GnomAD4 genome

AF:

0.00549

AC:

837

AN:

152322

Hom.:

Cov.:

AF XY:

0.00513

AC XY:

382

AN XY:

74480

show subpopulations

Gnomad4 AFR

AF:

0.00115

Gnomad4 AMR

AF:

0.00458

Gnomad4 ASJ

AF:

0.00202

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00766

Gnomad4 FIN

AF:

0.00207

Gnomad4 NFE

AF:

0.00901

Gnomad4 OTH

AF:

0.00378

Alfa

AF:

0.00695

Hom.:

Bravo

AF:

0.00511

Asia WGS

AF:

0.00231

AC:

AN:

3478

EpiCase

AF:

0.0110

EpiControl

AF:

0.0107

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.36

CADD

Benign

DANN

Benign

0.90

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.26

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.26

Position offset: 31

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over