rs925114

Positions:

• chr15-79413177-A-G

Variant summary

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

The XM_011521392.2(MINAR1):​c.-431A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 152,088 control chromosomes in the GnomAD database, including 14,297 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 0.43 (14293 hom., cov: 32)
  • Exomes 𝑓: 0.75 (4 hom.)
• Consequence: MINAR1 XM_011521392.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

Genes affected

MINAR1 (HGNC:):

TMED3 (HGNC:28889): (transmembrane p24 trafficking protein 3) Predicted to be involved in Golgi organization; endoplasmic reticulum to Golgi vesicle-mediated transport; and intracellular protein transport. Located in Golgi apparatus; endoplasmic reticulum; and endoplasmic reticulum-Golgi intermediate compartment. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MINAR1	XM_011521392.2	c.-431A>G		5_prime_UTR_variant	1/4
TMED3	NM_001330376.2	c.*1673A>G		3_prime_UTR_variant	3/3
MINAR1	XM_017022027.2	c.-51+1537A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMED3	ENST00000424155.6	c.*1673A>G		3_prime_UTR_variant	3/3	3

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64912 AN: 151958 Hom.: 14291 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.447

GnomAD4 exome AF: 0.750 AC: 9 AN: 12 Hom.: 4 Cov.: 0 AF XY: 0.700 AC XY: 7 AN XY: 10

Gnomad4 NFE exome AF: 0.700

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.427 AC: 64918 AN: 152076 Hom.: 14293 Cov.: 32 AF XY: 0.421 AC XY: 31276 AN XY: 74334

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.519

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.445

Alfa AF: 0.472 Hom.: 19086

Bravo AF: 0.417

Asia WGS AF: 0.410 AC: 1427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.5
DANN	Benign	0.81

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs925114; hg19: chr15-79705519;