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GeneBe

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

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.442

Links

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
FGFR2NM_000141.5 linkuse as main transcriptc.109+7033T>C intron_variant ENST00000358487.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FGFR2ENST00000358487.10 linkuse as main transcriptc.109+7033T>C intron_variant 1 NM_000141.5 A2P21802-1

Frequencies

GnomAD3 genomes
AF:
0.408
AC:
62043
AN:
151932
Hom.:
12679
Cov.:
33
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 submitterclinical testingInvitaeNov 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.

Other links and lift over

dbSNP: rs1219648; hg19: chr10-123346190;