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GeneBe

6-79446542-C-T

Variant summary

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

The XR_942714.3(LOC105377867):n.381G>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 0.233 in 152,026 control chromosomes in the GnomAD database, including 4,604 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 0.23 ( 4604 hom., cov: 33)

Consequence

LOC105377867
XR_942714.3 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.322
Variant links:
Genes affected

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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=-0.9).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105377867XR_942714.3 linkuse as main transcriptn.381G>A non_coding_transcript_exon_variant 1/3
LOC100506851XR_001744215.3 linkuse as main transcriptn.1825+24339C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000652956.1 linkuse as main transcriptn.184+24339C>T intron_variant, non_coding_transcript_variant
ENST00000653204.1 linkuse as main transcriptn.527-6969C>T intron_variant, non_coding_transcript_variant
ENST00000653689.1 linkuse as main transcriptn.1497+24339C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.233
AC:
35391
AN:
151906
Hom.:
4607
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.146
Gnomad AMI
AF:
0.340
Gnomad AMR
AF:
0.181
Gnomad ASJ
AF:
0.321
Gnomad EAS
AF:
0.0740
Gnomad SAS
AF:
0.348
Gnomad FIN
AF:
0.273
Gnomad MID
AF:
0.236
Gnomad NFE
AF:
0.288
Gnomad OTH
AF:
0.256
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:
0.233
AC:
35384
AN:
152026
Hom.:
4604
Cov.:
33
AF XY:
0.230
AC XY:
17124
AN XY:
74296
show subpopulations
Gnomad4 AFR
AF:
0.146
Gnomad4 AMR
AF:
0.181
Gnomad4 ASJ
AF:
0.321
Gnomad4 EAS
AF:
0.0739
Gnomad4 SAS
AF:
0.347
Gnomad4 FIN
AF:
0.273
Gnomad4 NFE
AF:
0.288
Gnomad4 OTH
AF:
0.253
Alfa
AF:
0.202
Hom.:
887
Bravo
AF:
0.218

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
Cadd
Benign
1.8
Dann
Benign
0.71

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: rs12204683; hg19: chr6-80156259; API