rs4244480

Variant summary

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

The ENST00000419556.2(THEM7P):​n.292+35423A>G 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 0.536 in 152,072 control chromosomes in the GnomAD database, including 23,797 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 0.54 ( 23797 hom., cov: 32)

Consequence

THEM7P
ENST00000419556.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0590
Variant links:
Genes affected
THEM7P (HGNC:50386): (thioesterase superfamily member 7, pseudogene)

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=-0.75).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.782 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
THEM7PENST00000419556.2 linkuse as main transcriptn.292+35423A>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.536
AC:
81376
AN:
151956
Hom.:
23756
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.789
Gnomad AMI
AF:
0.377
Gnomad AMR
AF:
0.454
Gnomad ASJ
AF:
0.526
Gnomad EAS
AF:
0.491
Gnomad SAS
AF:
0.561
Gnomad FIN
AF:
0.417
Gnomad MID
AF:
0.494
Gnomad NFE
AF:
0.423
Gnomad OTH
AF:
0.538
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.536
AC:
81481
AN:
152072
Hom.:
23797
Cov.:
32
AF XY:
0.535
AC XY:
39781
AN XY:
74336
show subpopulations
Gnomad4 AFR
AF:
0.789
Gnomad4 AMR
AF:
0.453
Gnomad4 ASJ
AF:
0.526
Gnomad4 EAS
AF:
0.491
Gnomad4 SAS
AF:
0.562
Gnomad4 FIN
AF:
0.417
Gnomad4 NFE
AF:
0.423
Gnomad4 OTH
AF:
0.538
Alfa
AF:
0.481
Hom.:
2485
Bravo
AF:
0.546
Asia WGS
AF:
0.593
AC:
2061
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
CADD
Benign
4.4
DANN
Benign
0.78

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: rs4244480; hg19: chr11-32216243; API