rs1219648

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_000141(FGFR2):c.109+7033T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 151932 control chromosomes in the gnomAD Genomes database, including 12679 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.41 ( 12679 hom., cov: 33)

Consequence

FGFR2
NM_000141 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.442

Links

FGFR2 (HGNC:3689):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BP6

Variant 10:121586676-A>G is Benign according to our data. Variant chr10-121586676-A-G is described in ClinVar as [Benign]. Clinvar id is 1663397. Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FGFR2	NM_000141.5 linkuse as main transcript	c.109+7033T>C		intron_variant		ENST00000358487.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FGFR2	ENST00000358487.10 linkuse as main transcript	c.109+7033T>C		intron_variant		1	NM_000141.5	A2	P21802-1

Frequencies

GnomAD3 genomes

AF:

0.408

AC:

62043

AN:

151932

Hom.:

12679

Cov.:

show subpopulations

Gnomad AFR

AF:

0.427

Gnomad AMI

AF:

0.548

Gnomad AMR

AF:

0.411

Gnomad ASJ

AF:

0.416

Gnomad EAS

AF:

0.379

Gnomad SAS

AF:

0.386

Gnomad FIN

AF:

0.431

Gnomad MID

AF:

0.446

Gnomad NFE

AF:

0.395

Gnomad OTH

AF:

0.408

Alfa

AF:

0.396

Hom.:

22831

Bravo

AF:

0.408

Asia WGS

AF:

0.372

AC:

1294

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

FGFR2-related craniosynostosis

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Nov 01, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

Cadd

Benign

0.71

Dann

Benign

0.74

Splicing

Find out SpliceAI 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

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over