Variant chr1-173475506-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_037845.1(LOC100506023):n.524+1126A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.951 in 152,308 control chromosomes in the GnomAD database, including 69,313 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 0.95 ( 69313 hom., cov: 33)

Consequence

LOC100506023
NR_037845.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.317

Variant links:

Genes affected

PRDX6-AS1 (HGNC:):

PRDX6-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100506023	NR_037845.1 linkuse as main transcript	n.524+1126A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect
PRDX6-AS1	ENST00000659863.1 linkuse as main transcript	n.250+2314A>G	intron_variant
PRDX6-AS1	ENST00000660739.1 linkuse as main transcript	n.365+1126A>G	intron_variant
PRDX6-AS1	ENST00000661267.1 linkuse as main transcript	n.540+1126A>G	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.951

AC:

144709

AN:

152190

Hom.:

69274

Cov.:

show subpopulations

Gnomad AFR

AF:

0.828

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.982

Gnomad ASJ

AF:

1.00

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.999

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

0.984

Gnomad NFE

AF:

1.00

Gnomad OTH

AF:

0.971

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

GnomAD4 genome

AF:

0.951

AC:

144804

AN:

152308

Hom.:

69313

Cov.:

AF XY:

0.952

AC XY:

70910

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.828

Gnomad4 AMR

AF:

0.982

Gnomad4 ASJ

AF:

1.00

Gnomad4 EAS

AF:

1.00

Gnomad4 SAS

AF:

0.999

Gnomad4 FIN

AF:

1.00

Gnomad4 NFE

AF:

1.00

Gnomad4 OTH

AF:

0.972

Alfa

AF:

0.969

Hom.:

8914

Bravo

AF:

0.944

Asia WGS

AF:

0.992

AC:

3449

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

3.5

DANN

Benign

0.51

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over