rs715301

Variant names:

• chr7-29575725-C-T
• rs715301
• ENST00000748764.1:n.425+23014G>A

Variant summary

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

The ENST00000748764.1(PRR15-DT):​n.425+23014G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,140 control chromosomes in the GnomAD database, including 1,129 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 0.11 (1129 hom., cov: 32)
• Consequence: PRR15-DT ENST00000748764.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.273
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000748764.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRR15-DT	ENST00000748764.1		n.425+23014G>A		intron	N/A
	PRR15-DT	ENST00000748765.1		n.424+23014G>A		intron	N/A
	PRR15-DT	ENST00000748766.1		n.408+23014G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16658 AN: 152022 Hom.: 1128 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0562

Gnomad ASJ AF: 0.0804

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.0978

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0725

Gnomad OTH AF: 0.0915

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

GnomAD4 genome AF: 0.110 AC: 16665 AN: 152140 Hom.: 1129 Cov.: 32 AF XY: 0.110 AC XY: 8181 AN XY: 74404

African (AFR) AF: 0.186 AC: 7694 AN: 41458

American (AMR) AF: 0.0561 AC: 858 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0804 AC: 279 AN: 3472

East Asian (EAS) AF: 0.220 AC: 1137 AN: 5172

South Asian (SAS) AF: 0.0975 AC: 470 AN: 4820

European-Finnish (FIN) AF: 0.101 AC: 1070 AN: 10598

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0725 AC: 4929 AN: 67998

Other (OTH) AF: 0.0905 AC: 191 AN: 2110

Alfa AF: 0.101 Hom.: 108

Bravo AF: 0.111

Asia WGS AF: 0.184 AC: 640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.6
DANN	Benign	0.38
PhyloP100		0.27

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: rs715301;

hg19: chr7-29615341;