rs6978690

Variant names:

• chr7-29551813-C-A
• rs6978690
• ENST00000447171.4:n.384+10046G>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000604053.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRR15-DT	NR_183547.1		n.368+10046G>T		intron	N/A
	PRR15-DT	NR_183548.1		n.109+10046G>T		intron	N/A
	PRR15-DT	NR_183549.1		n.45+11834G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRR15-DT	ENST00000447171.4	TSL:1	n.384+10046G>T		intron	N/A
	GTF3C6P3	ENST00000604053.1	TSL:6	n.293C>A		non_coding_transcript_exon	Exon 1 of 1
	PRR15-DT	ENST00000450540.4	TSL:3	n.316+11575G>T		intron	N/A

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

African (AFR) AF: 0.259 AC: 442 AN: 1706

American (AMR) AF: 0.0783 AC: 456 AN: 5822

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 137 AN: 870

East Asian (EAS) AF: 0.278 AC: 986 AN: 3542

South Asian (SAS) AF: 0.231 AC: 1431 AN: 6202

European-Finnish (FIN) AF: 0.0946 AC: 1320 AN: 13956

Middle Eastern (MID) AF: 0.225 AC: 18 AN: 80

European-Non Finnish (NFE) AF: 0.152 AC: 4398 AN: 28848

Other (OTH) AF: 0.126 AC: 306 AN: 2428

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

African (AFR) AF: 0.257 AC: 10641 AN: 41466

American (AMR) AF: 0.158 AC: 2413 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 613 AN: 3470

East Asian (EAS) AF: 0.311 AC: 1605 AN: 5154

South Asian (SAS) AF: 0.245 AC: 1178 AN: 4808

European-Finnish (FIN) AF: 0.110 AC: 1165 AN: 10582

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11345 AN: 67978

Other (OTH) AF: 0.201 AC: 424 AN: 2110

Alfa AF: 0.175 Hom.: 4275

Bravo AF: 0.201

Asia WGS AF: 0.268 AC: 930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.49
PhyloP100		1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6978690;

hg19: chr7-29591429;