7-34295479-C-T

Variant summary

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

The ENST00000660587.1(ENSG00000236212):​n.167-2100C>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 0.374 in 151,776 control chromosomes in the GnomAD database, including 10,708 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 0.37 ( 10708 hom., cov: 32)

Consequence


ENST00000660587.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.44
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=-0.91).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.435 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
ENST00000660587.1 linkuse as main transcriptn.167-2100C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.374
AC:
56666
AN:
151658
Hom.:
10686
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.364
Gnomad AMI
AF:
0.341
Gnomad AMR
AF:
0.444
Gnomad ASJ
AF:
0.343
Gnomad EAS
AF:
0.439
Gnomad SAS
AF:
0.259
Gnomad FIN
AF:
0.352
Gnomad MID
AF:
0.310
Gnomad NFE
AF:
0.372
Gnomad OTH
AF:
0.384
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.374
AC:
56731
AN:
151776
Hom.:
10708
Cov.:
32
AF XY:
0.374
AC XY:
27690
AN XY:
74134
show subpopulations
Gnomad4 AFR
AF:
0.364
Gnomad4 AMR
AF:
0.444
Gnomad4 ASJ
AF:
0.343
Gnomad4 EAS
AF:
0.439
Gnomad4 SAS
AF:
0.259
Gnomad4 FIN
AF:
0.352
Gnomad4 NFE
AF:
0.372
Gnomad4 OTH
AF:
0.389
Alfa
AF:
0.369
Hom.:
5698
Bravo
AF:
0.384
Asia WGS
AF:
0.364
AC:
1267
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.31
DANN
Benign
0.42

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: rs2058163; hg19: chr7-34335091; API