1-173489187-C-T

Variant names:

• chr1-173489187-C-T
• rs33951697
• XR_007066738.1:n.3620G>A

Variant summary

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

The XR_007066738.1(LOC124904456):​n.3620G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,138 control chromosomes in the GnomAD database, including 2,009 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 0.15 (2009 hom., cov: 32)
• Consequence: LOC124904456 XR_007066738.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.807
• Publications: 4 publications found

Genes affected

LOC124904456 (HGNC:):

PRDX6-AS1 (HGNC:54870): (PRDX6 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904456	XR_007066738.1	n.3620G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRDX6-AS1	ENST00000669220.1	n.117+104G>A		intron_variant	Intron 1 of 3
PRDX6-AS1	ENST00000778745.1	n.112+104G>A		intron_variant	Intron 1 of 2
PRDX6-AS1	ENST00000778747.1	n.114+104G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22548 AN: 152020 Hom.: 2008 Cov.: 32

Gnomad AFR AF: 0.0537

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.148 AC: 22561 AN: 152138 Hom.: 2009 Cov.: 32 AF XY: 0.148 AC XY: 10982 AN XY: 74360

African (AFR) AF: 0.0537 AC: 2230 AN: 41536

American (AMR) AF: 0.162 AC: 2469 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 984 AN: 3462

East Asian (EAS) AF: 0.312 AC: 1610 AN: 5164

South Asian (SAS) AF: 0.120 AC: 579 AN: 4824

European-Finnish (FIN) AF: 0.136 AC: 1436 AN: 10566

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12658 AN: 67986

Other (OTH) AF: 0.154 AC: 325 AN: 2112

Alfa AF: 0.170 Hom.: 465

Bravo AF: 0.148

Asia WGS AF: 0.189 AC: 655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.51
DANN	Benign	0.48
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs33951697; hg19: chr1-173458326; COSMIC: COSV107424399;