chr17-62944250-A-G

Position:

• chr17-62944250-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_030363.1(MIR633):​n.36A>G 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 0.0283 in 533,120 control chromosomes in the GnomAD database, including 303 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 0.028 (78 hom., cov: 32)
  • Exomes 𝑓: 0.028 (225 hom.)
• Consequence: MIR633 NR_030363.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.464

Genes affected

MIR633 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0278 (4232/152286) while in subpopulation SAS AF= 0.0367 (177/4824). AF 95% confidence interval is 0.0323. There are 78 homozygotes in gnomad4. There are 2069 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 78 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR633	NR_030363.1	n.36A>G		non_coding_transcript_exon_variant	1/1
MIR633	unassigned_transcript_3076	n.-25A>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR633	ENST00000384821.1	n.36A>G		non_coding_transcript_exon_variant	1/1	6
ENSG00000283538	ENST00000636248.2	n.51-7385T>C		intron_variant		5
ENSG00000283538	ENST00000650312.1	n.128-7385T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0277 AC: 4221 AN: 152168 Hom.: 77 Cov.: 32

Gnomad AFR AF: 0.0313

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0195

Gnomad ASJ AF: 0.00864

Gnomad EAS AF: 0.00557

Gnomad SAS AF: 0.0360

Gnomad FIN AF: 0.0382

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0278

Gnomad OTH AF: 0.0263

GnomAD3 exomes AF: 0.0258 AC: 6348 AN: 245632 Hom.: 106 AF XY: 0.0268 AC XY: 3565 AN XY: 133182

Gnomad AFR exome AF: 0.0325

Gnomad AMR exome AF: 0.0113

Gnomad ASJ exome AF: 0.0103

Gnomad EAS exome AF: 0.00618

Gnomad SAS exome AF: 0.0365

Gnomad FIN exome AF: 0.0357

Gnomad NFE exome AF: 0.0290

Gnomad OTH exome AF: 0.0296

GnomAD4 exome AF: 0.0284 AC: 10833 AN: 380834 Hom.: 225 Cov.: 0 AF XY: 0.0297 AC XY: 6437 AN XY: 216822

Gnomad4 AFR exome AF: 0.0333

Gnomad4 AMR exome AF: 0.0110

Gnomad4 ASJ exome AF: 0.0109

Gnomad4 EAS exome AF: 0.00502

Gnomad4 SAS exome AF: 0.0371

Gnomad4 FIN exome AF: 0.0351

Gnomad4 NFE exome AF: 0.0293

Gnomad4 OTH exome AF: 0.0317

GnomAD4 genome AF: 0.0278 AC: 4232 AN: 152286 Hom.: 78 Cov.: 32 AF XY: 0.0278 AC XY: 2069 AN XY: 74458

Gnomad4 AFR AF: 0.0313

Gnomad4 AMR AF: 0.0195

Gnomad4 ASJ AF: 0.00864

Gnomad4 EAS AF: 0.00559

Gnomad4 SAS AF: 0.0367

Gnomad4 FIN AF: 0.0382

Gnomad4 NFE AF: 0.0278

Gnomad4 OTH AF: 0.0275

Alfa AF: 0.0279 Hom.: 31

Bravo AF: 0.0260

Asia WGS AF: 0.0340 AC: 119 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.0
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17759989; hg19: chr17-61021611;