3-75665296-C-T

Variant names:

• chr3-75665296-C-T
• rs75613762
• NM_001124759.5:c.334+93C>T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_001124759.5(FRG2C):​c.334+93C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.50 (0 hom., cov: 53)
  • Exomes 𝑓: 0.38 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: FRG2C NM_001124759.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.08

Genes affected

FRG2C (HGNC:33626): (FSHD region gene 2 family member C) Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

RPL23AP49 (HGNC:35689): (ribosomal protein L23a pseudogene 49)

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BP6: Variant 3-75665296-C-T is Benign according to our data. Variant chr3-75665296-C-T is described in ClinVar as [Benign]. Clinvar id is 982117.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FRG2C	NM_001124759.5	c.334+93C>T		intron_variant	Intron 3 of 3	ENST00000308062.8	NP_001118231.1
FRG2C	NM_001410775.1	c.331+93C>T		intron_variant	Intron 3 of 3		NP_001397704.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FRG2C	ENST00000308062.8	c.334+93C>T		intron_variant	Intron 3 of 3	1	NM_001124759.5	ENSP00000312299.3
FRG2C	ENST00000464571.1	c.331+93C>T		intron_variant	Intron 3 of 3	1		ENSP00000419432.1
RPL23AP49	ENST00000638439.1	n.137+4724G>A		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.00 AC: 74228 AN: 148690 Hom.: 0 Cov.: 53 FAILED QC

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.500

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.377 AC: 294593 AN: 781280 Hom.: 0 AF XY: 0.386 AC XY: 155437 AN XY: 402946

Gnomad4 AFR exome AF: 0.400

Gnomad4 AMR exome AF: 0.439

Gnomad4 ASJ exome AF: 0.448

Gnomad4 EAS exome AF: 0.468

Gnomad4 SAS exome AF: 0.437

Gnomad4 FIN exome AF: 0.484

Gnomad4 NFE exome AF: 0.346

Gnomad4 OTH exome AF: 0.410

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.499 AC: 74271 AN: 148782 Hom.: 0 Cov.: 53 AF XY: 0.499 AC XY: 36273 AN XY: 72662

Gnomad4 AFR AF: 0.498

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.500

Gnomad4 EAS AF: 0.500

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.499

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.500

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

-

Pathology and Clinical Laboratory Medicine, King Fahad Medical City

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.3
DANN	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs75613762; hg19: chr3-75714447;