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GeneBe

rs2981582

Variant summary

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

The NM_000141.5(FGFR2):c.109+906T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 151778 control chromosomes in the gnomAD Genomes database, including 26072 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.58 ( 26072 hom., cov: 31)

Consequence

FGFR2
NM_000141.5 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.827

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP6
?
Variant 10-121592803-A-G is Benign according to our data. Variant chr10-121592803-A-G is described in ClinVar as [Benign]. Clinvar id is 36931. Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FGFR2NM_000141.5 linkuse as main transcriptc.109+906T>C intron_variant ENST00000358487.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FGFR2ENST00000358487.10 linkuse as main transcriptc.109+906T>C intron_variant 1 NM_000141.5 A2P21802-1

Frequencies

GnomAD3 genomes
AF:
0.584
AC:
88710
AN:
151778
Hom.:
26072
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.521
Gnomad AMI
AF:
0.436
Gnomad AMR
AF:
0.590
Gnomad ASJ
AF:
0.576
Gnomad EAS
AF:
0.689
Gnomad SAS
AF:
0.653
Gnomad FIN
AF:
0.578
Gnomad MID
AF:
0.554
Gnomad NFE
AF:
0.613
Gnomad OTH
AF:
0.585
Alfa
AF:
0.604
Hom.:
52956
Bravo
AF:
0.581
Asia WGS
AF:
0.665
AC:
2311
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
-0.49
Cadd
Benign
12
Dann
Benign
0.64

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2981582; hg19: chr10-123352317; COSMIC: COSV60638493;