Variant rs2981582 details in Genebe, Genetics Data Aggregator

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

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.827

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=-0.49).

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
FGFR2	NM_000141.5 linkuse as main transcript	c.109+906T>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+906T>C		intron_variant		1	NM_000141.5	A2	P21802-1

Frequencies

GnomAD3 genomes

AF:

0.584

AC:

88710

AN:

151778

Hom.:

26072

Cov.:

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 submitter

clinical testing

Invitae

Nov 01, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

Cadd

Benign

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.

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