7-29607992-G-C

Variant names:

• chr7-29607992-G-C
• rs10499589
• ENST00000748771.1:n.467C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000748771.1(PRR15-DT):​n.467C>G 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 0.0693 in 152,238 control chromosomes in the GnomAD database, including 574 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 0.069 (574 hom., cov: 33)
• Consequence: PRR15-DT ENST00000748771.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.806
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRR15-DT	ENST00000748771.1	n.467C>G		non_coding_transcript_exon_variant	Exon 2 of 4
PRR15-DT	ENST00000442865.1	n.484-9091C>G		intron_variant	Intron 1 of 1	4
PRR15-DT	ENST00000748764.1	n.263-9091C>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.0693 AC: 10548 AN: 152120 Hom.: 574 Cov.: 33

Gnomad AFR AF: 0.0145

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.0616

Gnomad ASJ AF: 0.0542

Gnomad EAS AF: 0.0121

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0903

Gnomad OTH AF: 0.0512

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

GnomAD4 genome AF: 0.0693 AC: 10547 AN: 152238 Hom.: 574 Cov.: 33 AF XY: 0.0733 AC XY: 5456 AN XY: 74432

African (AFR) AF: 0.0145 AC: 602 AN: 41570

American (AMR) AF: 0.0614 AC: 939 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0542 AC: 188 AN: 3470

East Asian (EAS) AF: 0.0122 AC: 63 AN: 5180

South Asian (SAS) AF: 0.117 AC: 565 AN: 4824

European-Finnish (FIN) AF: 0.166 AC: 1759 AN: 10592

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0903 AC: 6142 AN: 67998

Other (OTH) AF: 0.0502 AC: 106 AN: 2112

Alfa AF: 0.0854 Hom.: 101

Bravo AF: 0.0557

Asia WGS AF: 0.0510 AC: 178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.22
DANN	Benign	0.61
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs10499589; hg19: chr7-29647608;