rs2293131

Variant names:

• chr4-189821537-A-G
• rs2293131
• ENST00000508156.5:n.461T>C

Variant summary

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

The ENST00000511785.2(FRG1-DT):​n.554T>C 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 0.239 in 152,062 control chromosomes in the GnomAD database, including 5,918 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 0.24 (5918 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: FRG1-DT ENST00000511785.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117

Genes affected

FRG1-DT (HGNC:51590): (FRG1 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FRG1-DT	NR_149039.1	n.1406+43056T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FRG1-DT	ENST00000508156.5	n.461T>C		non_coding_transcript_exon_variant	Exon 4 of 4	3
FRG1-DT	ENST00000511785.2	n.554T>C		non_coding_transcript_exon_variant	Exon 3 of 3	2
FRG1-DT	ENST00000506276.5	n.240-40738T>C		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36285 AN: 151944 Hom.: 5909 Cov.: 32

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.0767

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.192

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.239 AC: 36332 AN: 152062 Hom.: 5918 Cov.: 32 AF XY: 0.234 AC XY: 17428 AN XY: 74358

Gnomad4 AFR AF: 0.473

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.0765

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.194

Alfa AF: 0.209 Hom.: 607

Bravo AF: 0.256

Asia WGS AF: 0.161 AC: 560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.60
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2293131; hg19: chr4-190742691;