Menu
GeneBe

6-88175102-C-T

Variant summary

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

The ENST00000624253.1(ENSG00000279565):n.2842C>T 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 0.798 in 152,196 control chromosomes in the GnomAD database, including 48,618 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 0.80 ( 48562 hom., cov: 30)
Exomes 𝑓: 0.75 ( 56 hom. )

Consequence


ENST00000624253.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.345
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=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.868 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
ENST00000624253.1 linkuse as main transcriptn.2842C>T non_coding_transcript_exon_variant 1/1

Frequencies

GnomAD3 genomes
AF:
0.798
AC:
121164
AN:
151880
Hom.:
48520
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.876
Gnomad AMI
AF:
0.785
Gnomad AMR
AF:
0.705
Gnomad ASJ
AF:
0.733
Gnomad EAS
AF:
0.778
Gnomad SAS
AF:
0.719
Gnomad FIN
AF:
0.747
Gnomad MID
AF:
0.782
Gnomad NFE
AF:
0.790
Gnomad OTH
AF:
0.795
GnomAD4 exome
AF:
0.747
AC:
148
AN:
198
Hom.:
56
Cov.:
0
AF XY:
0.771
AC XY:
108
AN XY:
140
show subpopulations
Gnomad4 AFR exome
AF:
0.750
Gnomad4 AMR exome
AF:
0.667
Gnomad4 ASJ exome
AF:
1.00
Gnomad4 EAS exome
AF:
0.667
Gnomad4 SAS exome
AF:
1.00
Gnomad4 FIN exome
AF:
0.500
Gnomad4 NFE exome
AF:
0.763
Gnomad4 OTH exome
AF:
0.750
GnomAD4 genome
AF:
0.798
AC:
121261
AN:
151998
Hom.:
48562
Cov.:
30
AF XY:
0.795
AC XY:
59078
AN XY:
74296
show subpopulations
Gnomad4 AFR
AF:
0.876
Gnomad4 AMR
AF:
0.705
Gnomad4 ASJ
AF:
0.733
Gnomad4 EAS
AF:
0.778
Gnomad4 SAS
AF:
0.718
Gnomad4 FIN
AF:
0.747
Gnomad4 NFE
AF:
0.790
Gnomad4 OTH
AF:
0.792
Alfa
AF:
0.782
Hom.:
60993
Bravo
AF:
0.798
Asia WGS
AF:
0.730
AC:
2542
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
Cadd
Benign
1.3
Dann
Benign
0.48

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: rs1406977; hg19: chr6-88884821; API