rs905508

chr15-69279329-C-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, non coding transcript 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: ENST00000558269.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.38

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=-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000558269.2	n.196-326C>T		intron_variant, non_coding_transcript_variant		2
PAQR5-DT	ENST00000570122.1	n.19-254G>A		intron_variant, non_coding_transcript_variant		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;