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GeneBe

rs2120991

Positions:

Variant summary

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

The ENST00000663306.1(ENSG00000286069):​n.573+1196C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 152,058 control chromosomes in the GnomAD database, including 6,846 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 0.27 ( 6846 hom., cov: 32)

Consequence


ENST00000663306.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.145
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC107984525XR_002957415.2 linkuse as main transcriptn.452-19753C>A intron_variant, non_coding_transcript_variant
LOC107984525XR_001749153.2 linkuse as main transcriptn.375+1196C>A intron_variant, non_coding_transcript_variant
LOC107984525XR_007063319.1 linkuse as main transcriptn.1494+1196C>A intron_variant, non_coding_transcript_variant
LOC107984525XR_007063320.1 linkuse as main transcriptn.322+1196C>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000663306.1 linkuse as main transcriptn.573+1196C>A intron_variant, non_coding_transcript_variant
ENST00000652339.1 linkuse as main transcriptn.509+15566C>A intron_variant, non_coding_transcript_variant
ENST00000654713.1 linkuse as main transcriptn.318-19753C>A intron_variant, non_coding_transcript_variant
ENST00000656247.1 linkuse as main transcriptn.345-19753C>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.272
AC:
41335
AN:
151938
Hom.:
6849
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0908
Gnomad AMI
AF:
0.393
Gnomad AMR
AF:
0.217
Gnomad ASJ
AF:
0.399
Gnomad EAS
AF:
0.157
Gnomad SAS
AF:
0.304
Gnomad FIN
AF:
0.314
Gnomad MID
AF:
0.266
Gnomad NFE
AF:
0.387
Gnomad OTH
AF:
0.270
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.272
AC:
41325
AN:
152058
Hom.:
6846
Cov.:
32
AF XY:
0.267
AC XY:
19835
AN XY:
74302
show subpopulations
Gnomad4 AFR
AF:
0.0905
Gnomad4 AMR
AF:
0.217
Gnomad4 ASJ
AF:
0.399
Gnomad4 EAS
AF:
0.157
Gnomad4 SAS
AF:
0.304
Gnomad4 FIN
AF:
0.314
Gnomad4 NFE
AF:
0.387
Gnomad4 OTH
AF:
0.269
Alfa
AF:
0.350
Hom.:
15958
Bravo
AF:
0.253
Asia WGS
AF:
0.232
AC:
810
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
1.6
DANN
Benign
0.33

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.

Other links and lift over

dbSNP: rs2120991; hg19: chr12-54270228; API