rs7171293

Variant names:

• chr15-69288082-G-A
• rs7171293
• ENST00000558269.2:n.405-326G>A

Your query was ambiguous. Multiple possible variants found:

• chr15-69288082-G-A
• chr15-69288082-G-T

Variant summary

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

The ENST00000558269.2(ENSG00000259504):​n.405-326G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0959 in 152,260 control chromosomes in the GnomAD database, including 745 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 0.096 (745 hom., cov: 32)
• Consequence: ENSG00000259504 ENST00000558269.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233
• Publications: 2 publications found

Genes affected

ENSG00000259504 (HGNC:):

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PAQR5-DT	NR_184009.1	n.394+340C>T		intron_variant	Intron 2 of 3
PAQR5-DT	NR_184010.1	n.394+340C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259504	ENST00000558269.2	n.405-326G>A		intron_variant	Intron 3 of 3	2
ENSG00000259504	ENST00000558454.2	n.171+3750G>A		intron_variant	Intron 1 of 1	3
PAQR5-DT	ENST00000565312.3	n.426+340C>T		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.0959 AC: 14592 AN: 152140 Hom.: 742 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0605

Gnomad ASJ AF: 0.0669

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.0929

Gnomad FIN AF: 0.0982

Gnomad MID AF: 0.0287

Gnomad NFE AF: 0.0963

Gnomad OTH AF: 0.0918

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

GnomAD4 genome AF: 0.0959 AC: 14599 AN: 152260 Hom.: 745 Cov.: 32 AF XY: 0.0938 AC XY: 6983 AN XY: 74444

African (AFR) AF: 0.106 AC: 4418 AN: 41560

American (AMR) AF: 0.0604 AC: 924 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0669 AC: 232 AN: 3468

East Asian (EAS) AF: 0.134 AC: 696 AN: 5176

South Asian (SAS) AF: 0.0919 AC: 443 AN: 4820

European-Finnish (FIN) AF: 0.0982 AC: 1040 AN: 10596

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0963 AC: 6550 AN: 68018

Other (OTH) AF: 0.0937 AC: 198 AN: 2114

Alfa AF: 0.0955 Hom.: 137

Bravo AF: 0.0916

Asia WGS AF: 0.123 AC: 428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.4
DANN	Benign	0.76
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs7171293; hg19: chr15-69580421;