13-32064729-A-G

Position:

• chr13-32064729-A-G

Variant summary

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

The NM_023037.3(FRY):​c.71-14105A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 152,098 control chromosomes in the GnomAD database, including 19,089 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 0.48 (19089 hom., cov: 32)
• Consequence: FRY NM_023037.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.947

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FRY	NM_023037.3	c.71-14105A>G		intron_variant		ENST00000542859.6	NP_075463.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FRY	ENST00000542859.6	c.71-14105A>G		intron_variant		5	NM_023037.3	ENSP00000445043	A1

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72751 AN: 151980 Hom.: 19075 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.479 AC: 72786 AN: 152098 Hom.: 19089 Cov.: 32 AF XY: 0.480 AC XY: 35699 AN XY: 74350

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.576

Gnomad4 OTH AF: 0.508

Alfa AF: 0.560 Hom.: 40527

Bravo AF: 0.467

Asia WGS AF: 0.454 AC: 1579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.70

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: rs390704; hg19: chr13-32638866; COSMIC: COSV66578283;