rs3

Positions:

• chr13-31872705-C-T

Variant summary

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

The XR_007063748.1(LOC124900336):​n.6395C>T variant causes a non coding transcript exon 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: LOC124900336 XR_007063748.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.637

Genes affected

LOC124900336 (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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900336	XR_007063748.1	n.6395C>T		non_coding_transcript_exon_variant	2/2
EEF1DP3	NR_027062.1	n.157+25766C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FRY	ENST00000428783.1	n.99+25766C>T		intron_variant, non_coding_transcript_variant		1
FRY	ENST00000645780.1	c.-254+25766C>T		intron_variant

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

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.0998

Gnomad4 ASJ AF: 0.0277

Gnomad4 EAS AF: 0.0421

Gnomad4 SAS AF: 0.0544

Gnomad4 FIN AF: 0.0420

Gnomad4 NFE AF: 0.0546

Gnomad4 OTH AF: 0.0847

Alfa AF: 0.0699 Hom.: 59

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	-0.89
CADD	Benign	7.3
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3; hg19: chr13-32446842;