rs905508

Variant names:

• chr15-69279329-C-T
• rs905508
• ENST00000558269.2:n.196-326C>T

Variant summary

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

The ENST00000558269.2(ENSG00000259504):​n.196-326C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,180 control chromosomes in the GnomAD database, including 1,621 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 0.14 (1621 hom., cov: 32)
• Consequence: ENSG00000259504 ENST00000558269.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.38

Genes affected

ENSG00000259504 (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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259504	ENST00000558269.2	n.196-326C>T		intron_variant	Intron 1 of 3	2
PAQR5-DT	ENST00000570122.1	n.19-254G>A		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21304 AN: 152062 Hom.: 1618 Cov.: 32

Gnomad AFR AF: 0.0977

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.140 AC: 21322 AN: 152180 Hom.: 1621 Cov.: 32 AF XY: 0.139 AC XY: 10359 AN XY: 74384

Gnomad4 AFR AF: 0.0979

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.145

Alfa AF: 0.154 Hom.: 2631

Bravo AF: 0.132

Asia WGS AF: 0.156 AC: 542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs905508; hg19: chr15-69571668;