ENST00000428783.1:n.100-38239T>G

Variant names:

• chr13-31903069-T-G
• rs362
• ENST00000428783.1:n.100-38239T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000428783.1(FRY):​n.100-38239T>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 ENST00000428783.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980
• Publications: 9 publications found

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]

EEF1DP3 (HGNC:30486): (eukaryotic translation elongation factor 1 delta pseudogene 3) Predicted to enable translation elongation factor activity. Predicted to be involved in translational elongation. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
EEF1DP3	NR_027062.1	n.158-42940T>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FRY	ENST00000428783.1	n.100-38239T>G		intron_variant	Intron 1 of 3	1
FRY	ENST00000645780.1	c.-253-42940T>G		intron_variant	Intron 1 of 61			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

African (AFR) AF: 0.759 AC: 31477 AN: 41448

American (AMR) AF: 0.555 AC: 8483 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2258 AN: 3468

East Asian (EAS) AF: 0.659 AC: 3392 AN: 5150

South Asian (SAS) AF: 0.726 AC: 3493 AN: 4810

European-Finnish (FIN) AF: 0.666 AC: 7035 AN: 10560

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.681 AC: 46262 AN: 67960

Other (OTH) AF: 0.667 AC: 1407 AN: 2110

Alfa AF: 0.666 Hom.: 5984

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
PhyloP100		-0.098

Splicing

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

Other links and lift over

dbSNP: rs362; hg19: chr13-32477206;