13-32035536-T-C

Position:

• chr13-32035536-T-C

Variant summary

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

The NM_023037.3(FRY):​c.70+3671T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0823 in 152,186 control chromosomes in the GnomAD database, including 1,526 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 0.082 (1526 hom., cov: 32)
• Consequence: FRY NM_023037.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.332

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]

FRY (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FRY	NM_023037.3	c.70+3671T>C		intron_variant		ENST00000542859.6	NP_075463.2
FRY	NM_001411012.1	c.70+3671T>C		intron_variant			NP_001397941.1
FRY	XM_047429999.1	c.70+3671T>C		intron_variant			XP_047285955.1
FRY	XM_047430000.1	c.70+3671T>C		intron_variant			XP_047285956.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FRY	ENST00000542859.6	c.70+3671T>C		intron_variant		5	NM_023037.3	ENSP00000445043.2

Frequencies

GnomAD3 genomes AF: 0.0822 AC: 12496 AN: 152068 Hom.: 1519 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0328

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0232

Gnomad FIN AF: 0.00254

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00798

Gnomad OTH AF: 0.0545

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

GnomAD4 genome AF: 0.0823 AC: 12532 AN: 152186 Hom.: 1526 Cov.: 32 AF XY: 0.0805 AC XY: 5995 AN XY: 74434

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.0328

Gnomad4 ASJ AF: 0.00173

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0230

Gnomad4 FIN AF: 0.00254

Gnomad4 NFE AF: 0.00798

Gnomad4 OTH AF: 0.0540

Alfa AF: 0.0315 Hom.: 111

Bravo AF: 0.0923

Asia WGS AF: 0.0290 AC: 101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.51

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: rs10492389; hg19: chr13-32609673;