6-34715858-G-A

Variant summary

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

The ENST00000334441.4(ENSG00000186328):​n.246G>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.845 in 170,734 control chromosomes in the GnomAD database, including 61,209 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 0.84 ( 53804 hom., cov: 30)
Exomes 𝑓: 0.89 ( 7405 hom. )

Consequence


ENST00000334441.4 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.14
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
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000334441.4 linkuse as main transcriptn.246G>A non_coding_transcript_exon_variant 1/1

Frequencies

GnomAD3 genomes
AF:
0.840
AC:
127613
AN:
151924
Hom.:
53764
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.794
Gnomad AMI
AF:
0.831
Gnomad AMR
AF:
0.881
Gnomad ASJ
AF:
0.832
Gnomad EAS
AF:
0.989
Gnomad SAS
AF:
0.920
Gnomad FIN
AF:
0.784
Gnomad MID
AF:
0.839
Gnomad NFE
AF:
0.851
Gnomad OTH
AF:
0.848
GnomAD4 exome
AF:
0.888
AC:
16591
AN:
18692
Hom.:
7405
Cov.:
0
AF XY:
0.892
AC XY:
9293
AN XY:
10420
show subpopulations
Gnomad4 AFR exome
AF:
0.856
Gnomad4 AMR exome
AF:
0.954
Gnomad4 ASJ exome
AF:
0.896
Gnomad4 EAS exome
AF:
0.992
Gnomad4 SAS exome
AF:
0.946
Gnomad4 FIN exome
AF:
0.813
Gnomad4 NFE exome
AF:
0.896
Gnomad4 OTH exome
AF:
0.898
GnomAD4 genome
AF:
0.840
AC:
127711
AN:
152042
Hom.:
53804
Cov.:
30
AF XY:
0.839
AC XY:
62339
AN XY:
74318
show subpopulations
Gnomad4 AFR
AF:
0.794
Gnomad4 AMR
AF:
0.881
Gnomad4 ASJ
AF:
0.832
Gnomad4 EAS
AF:
0.989
Gnomad4 SAS
AF:
0.921
Gnomad4 FIN
AF:
0.784
Gnomad4 NFE
AF:
0.851
Gnomad4 OTH
AF:
0.849
Alfa
AF:
0.831
Hom.:
7577
Bravo
AF:
0.844

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.72
CADD
Benign
7.3
DANN
Benign
0.67

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: rs6938239; hg19: chr6-34683635; API