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GeneBe

rs9379174

chr6-8222541-C-T

Variant summary

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

The ENST00000642149.1(ENSG00000232234):n.207-16390C>T 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 0.239 in 152,052 control chromosomes in the GnomAD database, including 4,452 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 0.24 ( 4452 hom., cov: 32)

Consequence


ENST00000642149.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.744
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=-0.98).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105374910XR_001743950.2 linkuse as main transcriptn.188-16390C>T intron_variant, non_coding_transcript_variant
LOC105374910XR_926440.3 linkuse as main transcriptn.81-7573C>T intron_variant, non_coding_transcript_variant
LOC105374910XR_926441.3 linkuse as main transcriptn.188-16390C>T intron_variant, non_coding_transcript_variant
LOC105374910XR_926443.3 linkuse as main transcriptn.81-16390C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000642149.1 linkuse as main transcriptn.207-16390C>T intron_variant, non_coding_transcript_variant
ENST00000439891.3 linkuse as main transcriptn.61-7573C>T intron_variant, non_coding_transcript_variant 5
ENST00000643749.1 linkuse as main transcriptn.143-16390C>T intron_variant, non_coding_transcript_variant
ENST00000647315.1 linkuse as main transcriptn.180-16390C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.239
AC:
36312
AN:
151934
Hom.:
4451
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.259
Gnomad AMI
AF:
0.289
Gnomad AMR
AF:
0.226
Gnomad ASJ
AF:
0.208
Gnomad EAS
AF:
0.365
Gnomad SAS
AF:
0.194
Gnomad FIN
AF:
0.193
Gnomad MID
AF:
0.241
Gnomad NFE
AF:
0.231
Gnomad OTH
AF:
0.263
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:
0.239
AC:
36330
AN:
152052
Hom.:
4452
Cov.:
32
AF XY:
0.236
AC XY:
17562
AN XY:
74332
show subpopulations
Gnomad4 AFR
AF:
0.259
Gnomad4 AMR
AF:
0.226
Gnomad4 ASJ
AF:
0.208
Gnomad4 EAS
AF:
0.366
Gnomad4 SAS
AF:
0.194
Gnomad4 FIN
AF:
0.193
Gnomad4 NFE
AF:
0.231
Gnomad4 OTH
AF:
0.263
Alfa
AF:
0.229
Hom.:
8264
Bravo
AF:
0.241
Asia WGS
AF:
0.251
AC:
873
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
Cadd
Benign
2.6
Dann
Benign
0.63

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: rs9379174; hg19: chr6-8222774; API