rs79049331

Variant names:

• chr1-173489421-C-T
• rs79049331
• XR_007066738.1:n.3386G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XR_007066738.1(LOC124904456):​n.3386G>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 0.00912 in 151,916 control chromosomes in the GnomAD database, including 19 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 0.0091 (19 hom., cov: 31)
• Consequence: LOC124904456 XR_007066738.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.17
• Publications: 0 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=-1.0).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00912 (1386/151916) while in subpopulation AFR AF = 0.0304 (1258/41396). AF 95% confidence interval is 0.029. There are 19 homozygotes in GnomAd4. There are 662 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 19 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000669220.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRDX6-AS1	ENST00000669220.1		n.-14G>A		upstream_gene	N/A
	PRDX6-AS1	ENST00000778745.1		n.-19G>A		upstream_gene	N/A
	PRDX6-AS1	ENST00000778747.1		n.-17G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.00905 AC: 1374 AN: 151798 Hom.: 19 Cov.: 31

Gnomad AFR AF: 0.0302

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.00512

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00187

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00637

Gnomad NFE AF: 0.000368

Gnomad OTH AF: 0.00577

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

GnomAD4 genome AF: 0.00912 AC: 1386 AN: 151916 Hom.: 19 Cov.: 31 AF XY: 0.00892 AC XY: 662 AN XY: 74250

African (AFR) AF: 0.0304 AC: 1258 AN: 41396

American (AMR) AF: 0.00524 AC: 80 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5164

South Asian (SAS) AF: 0.00167 AC: 8 AN: 4804

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10552

Middle Eastern (MID) AF: 0.00685 AC: 2 AN: 292

European-Non Finnish (NFE) AF: 0.000368 AC: 25 AN: 67964

Other (OTH) AF: 0.00571 AC: 12 AN: 2100

Alfa AF: 0.00704 Hom.: 0

Bravo AF: 0.0101

Asia WGS AF: 0.00346 AC: 12 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	0.30
DANN	Benign	0.72
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs79049331; hg19: chr1-173458560;