12-69574238-A-T

Variant names:

• chr12-69574238-A-T
• rs1881009924
• NM_001278356.2:c.810A>T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001278356.2(FRS2):​c.810A>T​(p.Gln270His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: FRS2 NM_001278356.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.20

Genes affected

FRS2 (HGNC:16971): (fibroblast growth factor receptor substrate 2) Enables fibroblast growth factor receptor binding activity and neurotrophin TRKA receptor binding activity. Involved in negative regulation of cardiac muscle cell differentiation. Acts upstream of or within fibroblast growth factor receptor signaling pathway. Located in adherens junction. Biomarker of renal cell carcinoma. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.09868482).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FRS2	NM_001278356.2	c.810A>T	p.Gln270His	missense_variant	Exon 9 of 9	ENST00000549921.6	NP_001265285.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FRS2	ENST00000549921.6	c.810A>T	p.Gln270His	missense_variant	Exon 9 of 9	1	NM_001278356.2	ENSP00000450048.1
FRS2	ENST00000550389.5	c.810A>T	p.Gln270His	missense_variant	Exon 7 of 7	1		ENSP00000447241.1
FRS2	ENST00000397997.6	c.810A>T	p.Gln270His	missense_variant	Exon 7 of 7	5		ENSP00000381083.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Aug 12, 2021

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.810A>T (p.Q270H) alteration is located in exon 10 (coding exon 5) of the FRS2 gene. This alteration results from a A to T substitution at nucleotide position 810, causing the glutamine (Q) at amino acid position 270 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.090
BayesDel_addAF	Benign	-0.18	T
BayesDel_noAF	Benign	-0.49
CADD	Benign	15
DANN	Benign	0.95
DEOGEN2	Benign	0.30	T;T;T
Eigen	Benign	-0.36
Eigen_PC	Benign	-0.19
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Benign	0.85	.;.;T
M_CAP	Benign	0.0073	T
MetaRNN	Benign	0.099	T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	-0.55	N;N;N
PrimateAI	Benign	0.38	T
PROVEAN	Benign	-0.58	N;N;N
REVEL	Benign	0.059
Sift	Benign	0.15	T;T;T
Sift4G	Benign	0.14	T;T;T
Polyphen		0.29	B;B;B
Vest4		0.12
MutPred		0.32		Gain of catalytic residue at D274 (P = 0.0098);Gain of catalytic residue at D274 (P = 0.0098);Gain of catalytic residue at D274 (P = 0.0098);
MVP		0.49
ClinPred		0.60	D
GERP RS		3.0
Varity_R		0.12
gMVP		0.21

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

Other links and lift over

dbSNP: rs1881009924; hg19: chr12-69968018;