rs905508

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558269.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259504	ENST00000558269.2	TSL:2	n.196-326C>T		intron	N/A
	PAQR5-DT	ENST00000570122.1	TSL:5	n.19-254G>A		intron	N/A
	PAQR5-DT	ENST00000746778.1		n.445+9093G>A		intron	N/A

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

African (AFR) AF: 0.0979 AC: 4065 AN: 41534

American (AMR) AF: 0.112 AC: 1715 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 466 AN: 3470

East Asian (EAS) AF: 0.154 AC: 793 AN: 5158

South Asian (SAS) AF: 0.111 AC: 533 AN: 4818

European-Finnish (FIN) AF: 0.195 AC: 2061 AN: 10582

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11148 AN: 68000

Other (OTH) AF: 0.145 AC: 305 AN: 2110

Alfa AF: 0.152 Hom.: 3522

Bravo AF: 0.132

Asia WGS AF: 0.156 AC: 542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.43
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs905508; hg19: chr15-69571668;