rs9854612

Variant summary

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

The ENST00000474255.1(TMED10P2):​n.352G>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 0.345 in 583,758 control chromosomes in the GnomAD database, including 38,054 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 0.40 ( 13722 hom., cov: 32)
Exomes 𝑓: 0.32 ( 24332 hom. )

Consequence

TMED10P2
ENST00000474255.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.53
Variant links:
Genes affected
TMED10P2 (HGNC:38105): (transmembrane p24 trafficking protein 10 pseudogene 2)

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=-0.67).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.595 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
TMED10P2ENST00000474255.1 linkuse as main transcriptn.352G>A non_coding_transcript_exon_variant 1/1

Frequencies

GnomAD3 genomes
AF:
0.401
AC:
60914
AN:
151832
Hom.:
13688
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.601
Gnomad AMI
AF:
0.363
Gnomad AMR
AF:
0.425
Gnomad ASJ
AF:
0.403
Gnomad EAS
AF:
0.463
Gnomad SAS
AF:
0.305
Gnomad FIN
AF:
0.270
Gnomad MID
AF:
0.449
Gnomad NFE
AF:
0.297
Gnomad OTH
AF:
0.395
GnomAD4 exome
AF:
0.325
AC:
140241
AN:
431806
Hom.:
24332
Cov.:
6
AF XY:
0.321
AC XY:
75963
AN XY:
236434
show subpopulations
Gnomad4 AFR exome
AF:
0.605
Gnomad4 AMR exome
AF:
0.437
Gnomad4 ASJ exome
AF:
0.407
Gnomad4 EAS exome
AF:
0.461
Gnomad4 SAS exome
AF:
0.301
Gnomad4 FIN exome
AF:
0.268
Gnomad4 NFE exome
AF:
0.294
Gnomad4 OTH exome
AF:
0.341
GnomAD4 genome
AF:
0.402
AC:
61011
AN:
151952
Hom.:
13722
Cov.:
32
AF XY:
0.400
AC XY:
29738
AN XY:
74264
show subpopulations
Gnomad4 AFR
AF:
0.601
Gnomad4 AMR
AF:
0.425
Gnomad4 ASJ
AF:
0.403
Gnomad4 EAS
AF:
0.463
Gnomad4 SAS
AF:
0.305
Gnomad4 FIN
AF:
0.270
Gnomad4 NFE
AF:
0.297
Gnomad4 OTH
AF:
0.397
Alfa
AF:
0.308
Hom.:
8259
Bravo
AF:
0.427
Asia WGS
AF:
0.398
AC:
1385
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.67
CADD
Benign
1.2
DANN
Benign
0.67

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: rs9854612; hg19: chr3-128257214; API