13-32007177-T-C

Position:

• chr13-32007177-T-C

Variant summary

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

The ENST00000647500.1(FRY):​c.205+60996T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 151,622 control chromosomes in the GnomAD database, including 1,614 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 0.11 (1614 hom., cov: 32)
• Consequence: FRY ENST00000647500.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.564

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FRY	ENST00000645780.1	c.-81+60996T>C		intron_variant				ENSP00000494080
FRY	ENST00000647500.1	c.205+60996T>C		intron_variant				ENSP00000494761

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16344 AN: 151504 Hom.: 1610 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0943

Gnomad ASJ AF: 0.0393

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0560

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0380

Gnomad OTH AF: 0.0849

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

GnomAD4 genome AF: 0.108 AC: 16362 AN: 151622 Hom.: 1614 Cov.: 32 AF XY: 0.110 AC XY: 8123 AN XY: 74046

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.0944

Gnomad4 ASJ AF: 0.0393

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.0560

Gnomad4 NFE AF: 0.0380

Gnomad4 OTH AF: 0.0864

Alfa AF: 0.0685 Hom.: 122

Bravo AF: 0.119

Asia WGS AF: 0.265 AC: 920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.54

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs457696; hg19: chr13-32581314;