rs4

Variant names:

• chr13-31873085-A-G
• rs4
• ENST00000428783.1:n.99+26146A>G

Variant summary

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

The ENST00000428783.1(FRY):​n.99+26146A>G 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 152,238 control chromosomes in the GnomAD database, including 894 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 (894 hom., cov: 32)
• Consequence: FRY ENST00000428783.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380
• 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900336	XR_007063748.1	n.6775A>G		non_coding_transcript_exon_variant	Exon 2 of 2
EEF1DP3	NR_027062.1	n.157+26146A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FRY	ENST00000428783.1	n.99+26146A>G		intron_variant	Intron 1 of 3	1
FRY	ENST00000645780.1	c.-254+26146A>G		intron_variant	Intron 1 of 61			ENSP00000494080.1

Frequencies

GnomAD3 genomes AF: 0.0906 AC: 13789 AN: 152120 Hom.: 891 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0997

Gnomad ASJ AF: 0.0277

Gnomad EAS AF: 0.0430

Gnomad SAS AF: 0.0544

Gnomad FIN AF: 0.0421

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0546

Gnomad OTH AF: 0.0833

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

GnomAD4 genome AF: 0.0907 AC: 13805 AN: 152238 Hom.: 894 Cov.: 32 AF XY: 0.0882 AC XY: 6567 AN XY: 74436

African (AFR) AF: 0.176 AC: 7298 AN: 41516

American (AMR) AF: 0.0997 AC: 1523 AN: 15280

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

East Asian (EAS) AF: 0.0429 AC: 222 AN: 5180

South Asian (SAS) AF: 0.0549 AC: 265 AN: 4830

European-Finnish (FIN) AF: 0.0421 AC: 447 AN: 10618

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

European-Non Finnish (NFE) AF: 0.0546 AC: 3714 AN: 68030

Other (OTH) AF: 0.0844 AC: 178 AN: 2110

Alfa AF: 0.0786 Hom.: 96

Bravo AF: 0.100

Asia WGS AF: 0.0660 AC: 228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.0
DANN	Benign	0.65
PhyloP100		-0.038

Splicing

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

Other links and lift over

dbSNP: rs4; hg19: chr13-32447222;