Variant 1-192790056-T-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000644058.1(ENSG00000285280):n.194-23862A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0984 in 152,058 control chromosomes in the GnomAD database, including 954 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 0.098 ( 954 hom., cov: 32)

Consequence

ENSG00000285280
ENST00000644058.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.49

Variant links:

Genes affected

ENSG00000285280 (HGNC:49018): (RSG2 antisense RNA 1)

ENSG00000285280 links:

LOC105371665 (HGNC:):

LOC105371665 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 (AFR) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371665	XR_922383.2 link	n.225+2243A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect
ENSG00000285280	ENST00000644058.1 link	n.194-23862A>C	intron_variant
ENSG00000285280	ENST00000644134.1 link	n.105-23862A>C	intron_variant
ENSG00000285280	ENST00000645822.1 link	n.369+2243A>C	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.0984

AC:

14953

AN:

151940

Hom.:

952

Cov.:

show subpopulations

Gnomad AFR

AF:

0.161

Gnomad AMI

AF:

0.0164

Gnomad AMR

AF:

0.125

Gnomad ASJ

AF:

0.100

Gnomad EAS

AF:

0.0763

Gnomad SAS

AF:

0.0436

Gnomad FIN

AF:

0.0310

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.0716

Gnomad OTH

AF:

0.0986

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

GnomAD4 genome

AF:

0.0984

AC:

14963

AN:

152058

Hom.:

954

Cov.:

AF XY:

0.0960

AC XY:

7135

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.161

Gnomad4 AMR

AF:

0.125

Gnomad4 ASJ

AF:

0.100

Gnomad4 EAS

AF:

0.0760

Gnomad4 SAS

AF:

0.0438

Gnomad4 FIN

AF:

0.0310

Gnomad4 NFE

AF:

0.0715

Gnomad4 OTH

AF:

0.0975

Alfa

AF:

0.0805

Hom.:

776

Bravo

AF:

0.109

Asia WGS

AF:

0.0690

AC:

242

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

0.19

DANN

Benign

0.79

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