NM_001004356.3:c.79+13G>T

Variant names:

• chr4-1012577-G-T
• rs1715655800
• NM_001004356.3:c.79+13G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Moderate BP6_Moderate

The NM_001004356.3(FGFRL1):​c.79+13G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000264 in 1,135,072 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 35)
  • Exomes 𝑓: 0.0000026 (0 hom.)
• Consequence: FGFRL1 NM_001004356.3 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.314
• Publications: 0 publications found

Genes affected

FGFRL1 (HGNC:3693): (fibroblast growth factor receptor like 1) The protein encoded by this gene is a member of the fibroblast growth factor receptor (FGFR) family, where amino acid sequence is highly conserved between members and throughout evolution. FGFR family members differ from one another in their ligand affinities and tissue distribution. A full-length representative protein would consist of an extracellular region, composed of three immunoglobulin-like domains, a single hydrophobic membrane-spanning segment and a cytoplasmic tyrosine kinase domain. The extracellular portion of the protein interacts with fibroblast growth factors, setting in motion a cascade of downstream signals, ultimately influencing mitogenesis and differentiation. A marked difference between this gene product and the other family members is its lack of a cytoplasmic tyrosine kinase domain. The result is a transmembrane receptor that could interact with other family members and potentially inhibit signaling. Multiple alternatively spliced transcript variants encoding the same isoform have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BP6: Variant 4-1012577-G-T is Benign according to our data. Variant chr4-1012577-G-T is described in ClinVar as Likely_benign. ClinVar VariationId is 1658544.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001004356.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FGFRL1	NM_001004356.3	MANE Select	c.79+13G>T		intron	N/A	NP_001004356.1	Q8N441
	FGFRL1	NM_001004358.1		c.79+13G>T		intron	N/A	NP_001004358.1	Q8N441
	FGFRL1	NM_001370296.1		c.79+13G>T		intron	N/A	NP_001357225.1	Q8N441

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FGFRL1	ENST00000510644.6	TSL:1 MANE Select	c.79+13G>T		intron	N/A	ENSP00000425025.1	Q8N441
	FGFRL1	ENST00000264748.6	TSL:1	c.79+13G>T		intron	N/A	ENSP00000264748.6	Q8N441
	FGFRL1	ENST00000504138.5	TSL:1	c.79+13G>T		intron	N/A	ENSP00000423091.1	Q8N441

Frequencies

GnomAD3 genomes Cov.: 35

GnomAD4 exome AF: 0.00000264 AC: 3 AN: 1135072 Hom.: 0 Cov.: 15 AF XY: 0.00000177 AC XY: 1 AN XY: 565714

African (AFR) AF: 0.00 AC: 0 AN: 23042

American (AMR) AF: 0.00 AC: 0 AN: 22670

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20250

East Asian (EAS) AF: 0.00 AC: 0 AN: 27782

South Asian (SAS) AF: 0.00 AC: 0 AN: 64892

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 33524

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4672

European-Non Finnish (NFE) AF: 0.00000337 AC: 3 AN: 889602

Other (OTH) AF: 0.00 AC: 0 AN: 48638

GnomAD4 genome Cov.: 35

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	13
DANN	Benign	0.93
PhyloP100		-0.31
PromoterAI		-0.013	Neutral

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

Other links and lift over

dbSNP: rs1715655800; hg19: chr4-1006365;