rs2075120

Variant summary

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

The ENST00000637740.1(ENSG00000283535):​n.340-377C>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 0.174 in 151,802 control chromosomes in the GnomAD database, including 2,848 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 0.17 ( 2848 hom., cov: 32)

Consequence


ENST00000637740.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.30
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=-1.01).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENST00000637740.1 linkuse as main transcriptn.340-377C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.174
AC:
26351
AN:
151686
Hom.:
2848
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0418
Gnomad AMI
AF:
0.278
Gnomad AMR
AF:
0.198
Gnomad ASJ
AF:
0.249
Gnomad EAS
AF:
0.213
Gnomad SAS
AF:
0.241
Gnomad FIN
AF:
0.177
Gnomad MID
AF:
0.272
Gnomad NFE
AF:
0.234
Gnomad OTH
AF:
0.188
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.174
AC:
26357
AN:
151802
Hom.:
2848
Cov.:
32
AF XY:
0.174
AC XY:
12942
AN XY:
74202
show subpopulations
Gnomad4 AFR
AF:
0.0417
Gnomad4 AMR
AF:
0.198
Gnomad4 ASJ
AF:
0.249
Gnomad4 EAS
AF:
0.212
Gnomad4 SAS
AF:
0.243
Gnomad4 FIN
AF:
0.177
Gnomad4 NFE
AF:
0.234
Gnomad4 OTH
AF:
0.189
Alfa
AF:
0.229
Hom.:
8486
Bravo
AF:
0.169
Asia WGS
AF:
0.214
AC:
745
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.6
DANN
Benign
0.51

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: rs2075120; hg19: chr22-17326432; API