rs7171293

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_184010.1(PAQR5-DT):​n.394+340C>T variant causes a intron, non coding transcript 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: PAQR5-DT NR_184010.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233

Genes affected

(HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
PAQR5-DT	NR_184010.1	n.394+340C>T		intron_variant, non_coding_transcript_variant
PAQR5-DT	NR_184009.1	n.394+340C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000558454.1	n.171+3750G>A		intron_variant, non_coding_transcript_variant		3
PAQR5-DT	ENST00000565312.3	n.426+340C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000558269.2	n.405-326G>A		intron_variant, non_coding_transcript_variant		2
PAQR5-DT	ENST00000570122.1	n.18+340C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.0604

Gnomad4 ASJ AF: 0.0669

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.0919

Gnomad4 FIN AF: 0.0982

Gnomad4 NFE AF: 0.0963

Gnomad4 OTH AF: 0.0937

Alfa AF: 0.0950 Hom.: 133

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7171293; hg19: chr15-69580421;