15-69272573-A-G

Variant names:

• chr15-69272573-A-G
• rs11633143
• ENST00000746778.1:n.446-7140T>C

Variant summary

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

The ENST00000746778.1(PAQR5-DT):​n.446-7140T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 152,184 control chromosomes in the GnomAD database, including 23,409 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 0.51 (23409 hom., cov: 32)
• Consequence: PAQR5-DT ENST00000746778.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 2 publications found

Genes affected

PAQR5-DT (HGNC:55353): (PAQR5 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000746778.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PAQR5-DT	ENST00000746778.1		n.446-7140T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77604 AN: 152066 Hom.: 23410 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.510 AC: 77593 AN: 152184 Hom.: 23409 Cov.: 32 AF XY: 0.514 AC XY: 38272 AN XY: 74398

African (AFR) AF: 0.164 AC: 6827 AN: 41534

American (AMR) AF: 0.655 AC: 10016 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2252 AN: 3472

East Asian (EAS) AF: 0.588 AC: 3045 AN: 5180

South Asian (SAS) AF: 0.570 AC: 2747 AN: 4818

European-Finnish (FIN) AF: 0.648 AC: 6857 AN: 10586

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.646 AC: 43902 AN: 67988

Other (OTH) AF: 0.545 AC: 1150 AN: 2110

Alfa AF: 0.551 Hom.: 3354

Bravo AF: 0.497

Asia WGS AF: 0.495 AC: 1720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.044
DANN	Benign	0.82
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs11633143; hg19: chr15-69564912;