5-109055959-C-T

Position:

• chr5-109055959-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005246.4(FER):​c.1924+8761C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 151,542 control chromosomes in the GnomAD database, including 2,106 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.16 (2106 hom., cov: 32)
• Consequence: FER NM_005246.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235

Genes affected

FER (HGNC:3655): (FER tyrosine kinase) The protein encoded by this gene is a member of the FPS/FES family of non-transmembrane receptor tyrosine kinases. It regulates cell-cell adhesion and mediates signaling from the cell surface to the cytoskeleton via growth factor receptors. Alternative splicing results in multiple transcript variants. A related pseudogene has been identified on chromosome X. [provided by RefSeq, Apr 2015]

FER (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FER	NM_005246.4	c.1924+8761C>T		intron_variant		ENST00000281092.9	NP_005237.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FER	ENST00000281092.9	c.1924+8761C>T		intron_variant		1	NM_005246.4	ENSP00000281092.4
FER	ENST00000618353.1	c.817+8761C>T		intron_variant		1		ENSP00000484767.1
FER	ENST00000438717.6	c.691+8761C>T		intron_variant		2		ENSP00000394297.4
FER	ENST00000504143.6	n.*1395+8761C>T		intron_variant		5		ENSP00000421951.2

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24646 AN: 151440 Hom.: 2103 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.0542

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.138

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.160

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.163 AC: 24663 AN: 151542 Hom.: 2106 Cov.: 32 AF XY: 0.162 AC XY: 11961 AN XY: 73994

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.0543

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.160

Alfa AF: 0.170 Hom.: 1185

Bravo AF: 0.154

Asia WGS AF: 0.102 AC: 352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.2
DANN	Benign	0.76

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: rs7719329; hg19: chr5-108391660;