Genetic Variant LOC124904456:n.3849C>G (chr1-173488958-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The XR_007066738.1(LOC124904456):n.3849C>G 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 0.0261 in 152,252 control chromosomes in the GnomAD database, including 66 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 0.026 ( 66 hom., cov: 32)

Consequence

LOC124904456
XR_007066738.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.47

Publications

1 publications found

Variant links:

Genes affected

LOC124904456 (HGNC:):

LOC124904456 links:

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

PRDX6-AS1 links:

PRDX6 (HGNC:16753): (peroxiredoxin 6) The protein encoded by this gene is a member of the thiol-specific antioxidant protein family. This protein is a bifunctional enzyme with two distinct active sites. It is involved in redox regulation of the cell; it can reduce H(2)O(2) and short chain organic, fatty acid, and phospholipid hydroperoxides. It may play a role in the regulation of phospholipid turnover as well as in protection against oxidative injury. [provided by RefSeq, Jul 2008]

PRDX6 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0261 (3969/152252) while in subpopulation NFE AF = 0.042 (2857/68012). AF 95% confidence interval is 0.0407. There are 66 homozygotes in GnomAd4. There are 1886 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 66 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904456	XR_007066738.1 link	n.3849C>G		non_coding_transcript_exon_variant	Exon 2 of 2
PRDX6	NM_004905.3 link	c.*1095G>C		downstream_gene_variant		ENST00000340385.6	NP_004896.1	P30041V9HWC7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
PRDX6-AS1	ENST00000669220.1 link	n.117+333C>G	intron_variant	Intron 1 of 3
PRDX6-AS1	ENST00000778745.1 link	n.112+333C>G	intron_variant	Intron 1 of 2
PRDX6-AS1	ENST00000778747.1 link	n.114+333C>G	intron_variant	Intron 1 of 1
PRDX6	ENST00000340385.6 link	c.*1095G>C	downstream_gene_variant		1	NM_004905.3	ENSP00000342026.5	P30041

Frequencies

GnomAD3 genomes

AF:

0.0261

AC:

3970

AN:

152134

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00763

Gnomad AMI

AF:

0.0680

Gnomad AMR

AF:

0.0143

Gnomad ASJ

AF:

0.0406

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00994

Gnomad FIN

AF:

0.0263

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0420

Gnomad OTH

AF:

0.0206

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

GnomAD4 genome

AF:

0.0261

AC:

3969

AN:

152252

Hom.:

Cov.:

AF XY:

0.0253

AC XY:

1886

AN XY:

74446

show subpopulations

African (AFR)

AF:

0.00761

AC:

316

AN:

41540

American (AMR)

AF:

0.0143

AC:

218

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0406

AC:

141

AN:

3470

East Asian (EAS)

AF:

0.000193

AC:

AN:

5192

South Asian (SAS)

AF:

0.00995

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.0263

AC:

279

AN:

10604

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0420

AC:

2857

AN:

68012

Other (OTH)

AF:

0.0204

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

212

424

635

847

1059

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

150

200

250

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0160

Hom.:

Bravo

AF:

0.0247

Asia WGS

AF:

0.00433

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.020

(source)

DANN

Benign

0.47

PhyloP100

-2.5

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over