Variant rs1025195 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_187952.1(LOC105375523):n.1630C>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 0.68 in 152,032 control chromosomes in the GnomAD database, including 35,391 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 0.68 ( 35391 hom., cov: 32)

Consequence

LOC105375523
NR_187952.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.62

Variant links:

Genes affected

ENSG00000232053 (HGNC:):

ENSG00000232053 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 = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
LOC105375523	NR_187952.1 linkuse as main transcript	n.1630C>A	non_coding_transcript_exon_variant	2/2
LOC105375523	NR_187953.1 linkuse as main transcript	n.1832C>A	non_coding_transcript_exon_variant	4/4
LOC105375523	NR_187954.1 linkuse as main transcript	n.1938C>A	non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
ENSG00000232053	ENST00000659747.1 linkuse as main transcript	n.1748C>A	non_coding_transcript_exon_variant	3/3
ENSG00000232053	ENST00000435996.1 linkuse as main transcript	n.242+66254C>A	intron_variant		3
ENSG00000232053	ENST00000445293.6 linkuse as main transcript	n.614+1296C>A	intron_variant		5

Frequencies

GnomAD3 genomes

AF:

0.680

AC:

103235

AN:

151914

Hom.:

35361

Cov.:

show subpopulations

Gnomad AFR

AF:

0.690

Gnomad AMI

AF:

0.664

Gnomad AMR

AF:

0.724

Gnomad ASJ

AF:

0.731

Gnomad EAS

AF:

0.873

Gnomad SAS

AF:

0.748

Gnomad FIN

AF:

0.552

Gnomad MID

AF:

0.725

Gnomad NFE

AF:

0.660

Gnomad OTH

AF:

0.698

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

GnomAD4 genome

AF:

0.680

AC:

103318

AN:

152032

Hom.:

35391

Cov.:

AF XY:

0.678

AC XY:

50395

AN XY:

74280

show subpopulations

Gnomad4 AFR

AF:

0.689

Gnomad4 AMR

AF:

0.725

Gnomad4 ASJ

AF:

0.731

Gnomad4 EAS

AF:

0.872

Gnomad4 SAS

AF:

0.748

Gnomad4 FIN

AF:

0.552

Gnomad4 NFE

AF:

0.660

Gnomad4 OTH

AF:

0.703

Alfa

AF:

0.673

Hom.:

16864

Bravo

AF:

0.695

Asia WGS

AF:

0.825

AC:

2866

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.057

DANN

Benign

0.52

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