4-87975096-G-T

Variant summary

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

The ENST00000662475.1(ENSG00000286618):​n.1074C>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 0.14 in 152,196 control chromosomes in the GnomAD database, including 2,166 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 0.14 ( 2166 hom., cov: 33)

Consequence

ENSG00000286618
ENST00000662475.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.180
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=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000286618ENST00000662475.1 linkn.1074C>A non_coding_transcript_exon_variant Exon 3 of 3

Frequencies

GnomAD3 genomes
AF:
0.140
AC:
21344
AN:
152078
Hom.:
2163
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.257
Gnomad AMI
AF:
0.187
Gnomad AMR
AF:
0.100
Gnomad ASJ
AF:
0.107
Gnomad EAS
AF:
0.365
Gnomad SAS
AF:
0.153
Gnomad FIN
AF:
0.132
Gnomad MID
AF:
0.165
Gnomad NFE
AF:
0.0628
Gnomad OTH
AF:
0.142
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.140
AC:
21372
AN:
152196
Hom.:
2166
Cov.:
33
AF XY:
0.146
AC XY:
10828
AN XY:
74414
show subpopulations
Gnomad4 AFR
AF:
0.257
Gnomad4 AMR
AF:
0.100
Gnomad4 ASJ
AF:
0.107
Gnomad4 EAS
AF:
0.365
Gnomad4 SAS
AF:
0.153
Gnomad4 FIN
AF:
0.132
Gnomad4 NFE
AF:
0.0628
Gnomad4 OTH
AF:
0.144
Alfa
AF:
0.0856
Hom.:
843
Bravo
AF:
0.144
Asia WGS
AF:
0.239
AC:
831
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
5.6
DANN
Benign
0.56

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: rs2853744; hg19: chr4-88896248; API