rs7586601

Positions:

• chr2-27361799-A-G

Variant summary

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

The NR_183825.1(GTF3C2-AS2):​n.1745+2339A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 151,914 control chromosomes in the GnomAD database, including 23,351 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 0.53 (23351 hom., cov: 30)
• Consequence: GTF3C2-AS2 NR_183825.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

Genes affected

GTF3C2-AS2 (HGNC:55699): (GTF3C2 antisense RNA 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GTF3C2-AS2	NR_183825.1	n.1745+2339A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GTF3C2-AS2	ENST00000412749.1	n.200+3897A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80153 AN: 151796 Hom.: 23285 Cov.: 30

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.529 AC: 80290 AN: 151914 Hom.: 23351 Cov.: 30 AF XY: 0.523 AC XY: 38855 AN XY: 74240

Gnomad4 AFR AF: 0.774

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.474

Alfa AF: 0.446 Hom.: 15500

Bravo AF: 0.542

Asia WGS AF: 0.372 AC: 1291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.81
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7586601; hg19: chr2-27584666;