3-128538371-G-A

Position:

• chr3-128538371-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

Genes affected

TMED10P2 (HGNC:38105): (transmembrane p24 trafficking protein 10 pseudogene 2)

ACMG classification

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
TMED10P2	ENST00000474255.1	n.352G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60914 AN: 151832 Hom.: 13688 Cov.: 32

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

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

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

Other links and lift over

dbSNP: rs9854612; hg19: chr3-128257214;