rs6978690

Variant names:

• chr7-29551813-C-A
• rs6978690
• ENST00000447171.3:n.383+10046G>T

Your query was ambiguous. Multiple possible variants found:

• chr7-29551813-C-A
• chr7-29551813-C-G

Variant summary

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

The ENST00000604053.1(GTF3C6P3):​n.293C>A 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 0.182 in 215,500 control chromosomes in the GnomAD database, including 4,041 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 0.20 (3227 hom., cov: 32)
  • Exomes 𝑓: 0.15 (814 hom.)
• Consequence: GTF3C6P3 ENST00000604053.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13

Genes affected

PRR15-DT (HGNC:55866): (PRR15 divergent transcript)

GTF3C6P3 (HGNC:55025): (GTF3C6 pseudogene 3)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GTF3C6P3		n.29551813C>A		intragenic_variant
PRR15-DT	NR_183547.1	n.368+10046G>T		intron_variant	Intron 2 of 2
PRR15-DT	NR_183548.1	n.109+10046G>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRR15-DT	ENST00000447171.3	n.383+10046G>T		intron_variant	Intron 2 of 2	1
GTF3C6P3	ENST00000604053.1	n.293C>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
PRR15-DT	ENST00000450540.3	n.304+11575G>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29650 AN: 151928 Hom.: 3217 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.200

GnomAD4 exome AF: 0.150 AC: 9494 AN: 63454 Hom.: 814 Cov.: 0 AF XY: 0.154 AC XY: 5578 AN XY: 36224

Gnomad4 AFR exome AF: 0.259

Gnomad4 AMR exome AF: 0.0783

Gnomad4 ASJ exome AF: 0.157

Gnomad4 EAS exome AF: 0.278

Gnomad4 SAS exome AF: 0.231

Gnomad4 FIN exome AF: 0.0946

Gnomad4 NFE exome AF: 0.152

Gnomad4 OTH exome AF: 0.126

GnomAD4 genome AF: 0.195 AC: 29691 AN: 152046 Hom.: 3227 Cov.: 32 AF XY: 0.195 AC XY: 14479 AN XY: 74340

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.201

Alfa AF: 0.164 Hom.: 2031

Bravo AF: 0.201

Asia WGS AF: 0.268 AC: 930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6978690; hg19: chr7-29591429;