13-32285286-C-G

Variant names:

• chr13-32285286-C-G
• rs114827
• NM_023037.3:c.8470-4347C>G

Variant summary

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

The NM_023037.3(FRY):​c.8470-4347C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 151,988 control chromosomes in the GnomAD database, including 4,156 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 0.21 (4156 hom., cov: 32)
• Consequence: FRY NM_023037.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.260

Genes affected

FRY (HGNC:20367): (FRY microtubule binding protein) Predicted to enable enzyme inhibitor activity. Predicted to be involved in cell morphogenesis and neuron projection development. Predicted to be located in microtubule organizing center and spindle pole. Predicted to be active in cell cortex and site of polarized growth. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FRY	NM_023037.3	c.8470-4347C>G		intron_variant	Intron 58 of 60	ENST00000542859.6	NP_075463.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FRY	ENST00000542859.6	c.8470-4347C>G		intron_variant	Intron 58 of 60	5	NM_023037.3	ENSP00000445043.2

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31659 AN: 151870 Hom.: 4160 Cov.: 32

Gnomad AFR AF: 0.0543

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0399

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.208 AC: 31649 AN: 151988 Hom.: 4156 Cov.: 32 AF XY: 0.207 AC XY: 15365 AN XY: 74310

Gnomad4 AFR AF: 0.0541

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.0398

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.230

Alfa AF: 0.122 Hom.: 226

Bravo AF: 0.202

Asia WGS AF: 0.115 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
DANN	Benign	0.69

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: rs114827; hg19: chr13-32859423;