rs12577592

Variant summary

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

The ENST00000419556.2(THEM7P):​n.292+43205A>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 0.141 in 152,186 control chromosomes in the GnomAD database, including 1,721 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 ( 1721 hom., cov: 32)

Consequence

THEM7P
ENST00000419556.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.50
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=-0.82).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.194 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
THEM7PENST00000419556.2 linkuse as main transcriptn.292+43205A>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.141
AC:
21481
AN:
152066
Hom.:
1721
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0526
Gnomad AMI
AF:
0.0987
Gnomad AMR
AF:
0.140
Gnomad ASJ
AF:
0.249
Gnomad EAS
AF:
0.196
Gnomad SAS
AF:
0.203
Gnomad FIN
AF:
0.147
Gnomad MID
AF:
0.176
Gnomad NFE
AF:
0.181
Gnomad OTH
AF:
0.153
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.141
AC:
21484
AN:
152186
Hom.:
1721
Cov.:
32
AF XY:
0.144
AC XY:
10727
AN XY:
74400
show subpopulations
Gnomad4 AFR
AF:
0.0525
Gnomad4 AMR
AF:
0.139
Gnomad4 ASJ
AF:
0.249
Gnomad4 EAS
AF:
0.196
Gnomad4 SAS
AF:
0.204
Gnomad4 FIN
AF:
0.147
Gnomad4 NFE
AF:
0.181
Gnomad4 OTH
AF:
0.151
Alfa
AF:
0.162
Hom.:
434
Bravo
AF:
0.134
Asia WGS
AF:
0.183
AC:
635
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
7.3
DANN
Benign
0.66

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: rs12577592; hg19: chr11-32208461; API