13-31903069-T-G

Position:

• chr13-31903069-T-G

Variant summary

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

The ENST00000645780.1(FRY):​c.-253-42940T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 151,984 control chromosomes in the GnomAD database, including 36,341 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 0.69 (36341 hom., cov: 31)
• Consequence: FRY ENST00000645780.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

Genes affected

FRY (HGNC:):

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EEF1DP3	NR_027062.1	n.158-42940T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FRY	ENST00000428783.1	n.100-38239T>G		intron_variant		1
FRY	ENST00000645780.1	c.-253-42940T>G		intron_variant				ENSP00000494080.1

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104622 AN: 151866 Hom.: 36290 Cov.: 31

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.796

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.689 AC: 104729 AN: 151984 Hom.: 36341 Cov.: 31 AF XY: 0.686 AC XY: 50984 AN XY: 74282

Gnomad4 AFR AF: 0.759

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.659

Gnomad4 SAS AF: 0.726

Gnomad4 FIN AF: 0.666

Gnomad4 NFE AF: 0.681

Gnomad4 OTH AF: 0.667

Alfa AF: 0.664 Hom.: 5769

Bravo AF: 0.679

Asia WGS AF: 0.697 AC: 2425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs362; hg19: chr13-32477206;