rs3

Variant names:

• chr13-31872705-C-T
• rs3
• ENST00000428783.1:n.99+25766C>T

Variant summary

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

The ENST00000428783.1(FRY):​n.99+25766C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0907 in 152,128 control chromosomes in the GnomAD database, including 892 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 0.091 (892 hom., cov: 32)
• Consequence: FRY ENST00000428783.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.637
• Publications: 0 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]

LOC124900336 (HGNC:):

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000428783.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EEF1DP3	NR_027062.1		n.157+25766C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FRY	ENST00000428783.1	TSL:1	n.99+25766C>T		intron	N/A
	FRY	ENST00000645780.1		c.-254+25766C>T		intron	N/A	ENSP00000494080.1

Frequencies

GnomAD3 genomes AF: 0.0907 AC: 13782 AN: 152010 Hom.: 889 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0999

Gnomad ASJ AF: 0.0277

Gnomad EAS AF: 0.0422

Gnomad SAS AF: 0.0539

Gnomad FIN AF: 0.0420

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0546

Gnomad OTH AF: 0.0837

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

GnomAD4 genome AF: 0.0907 AC: 13798 AN: 152128 Hom.: 892 Cov.: 32 AF XY: 0.0883 AC XY: 6564 AN XY: 74370

African (AFR) AF: 0.176 AC: 7299 AN: 41482

American (AMR) AF: 0.0998 AC: 1525 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0277 AC: 96 AN: 3468

East Asian (EAS) AF: 0.0421 AC: 218 AN: 5178

South Asian (SAS) AF: 0.0544 AC: 262 AN: 4820

European-Finnish (FIN) AF: 0.0420 AC: 445 AN: 10584

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0546 AC: 3712 AN: 68002

Other (OTH) AF: 0.0847 AC: 179 AN: 2114

Alfa AF: 0.0739 Hom.: 68

Bravo AF: 0.100

Asia WGS AF: 0.0660 AC: 228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.3
DANN	Benign	0.65
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs3; hg19: chr13-32446842;