7-29592311-C-T

Variant names:

• chr7-29592311-C-T
• rs10499585
• ENST00000748764.1:n.425+6428G>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+6428G>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 152,120 control chromosomes in the GnomAD database, including 1,171 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 (1171 hom., cov: 32)
• Consequence: PRR15-DT ENST00000748764.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.206 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+6428G>A		intron	N/A
	PRR15-DT	ENST00000748765.1		n.424+6428G>A		intron	N/A
	PRR15-DT	ENST00000748766.1		n.408+6428G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16658 AN: 152002 Hom.: 1168 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0556

Gnomad ASJ AF: 0.0806

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.0995

Gnomad FIN AF: 0.0931

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0712

Gnomad OTH AF: 0.0924

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

GnomAD4 genome AF: 0.110 AC: 16671 AN: 152120 Hom.: 1171 Cov.: 32 AF XY: 0.110 AC XY: 8154 AN XY: 74358

African (AFR) AF: 0.190 AC: 7886 AN: 41470

American (AMR) AF: 0.0554 AC: 848 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0806 AC: 280 AN: 3472

East Asian (EAS) AF: 0.216 AC: 1118 AN: 5164

South Asian (SAS) AF: 0.0992 AC: 478 AN: 4820

European-Finnish (FIN) AF: 0.0931 AC: 986 AN: 10586

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0712 AC: 4844 AN: 67996

Other (OTH) AF: 0.0915 AC: 193 AN: 2110

Alfa AF: 0.0719 Hom.: 252

Bravo AF: 0.111

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.37
PhyloP100		-0.070

Splicing

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

Other links and lift over

dbSNP: rs10499585; hg19: chr7-29631927;