rs41291173

Positions:

• chr2-55983005-G-A
• chr2-55983005-G-C

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BS1 BS2

The NR_029630.1(MIR217):​n.72C>T variant causes a non coding transcript exon change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0141 in 532,846 control chromosomes in the GnomAD database, including 86 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 0.014 (25 hom., cov: 32)
  • Exomes 𝑓: 0.014 (61 hom.)
• Consequence: MIR217 NR_029630.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.46

Genes affected

ENSG00000272180 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.18).
• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0141 (2152/152268) while in subpopulation AMR AF= 0.0275 (421/15310). AF 95% confidence interval is 0.0253. There are 25 homozygotes in gnomad4. There are 985 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 25 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR217	NR_029630.1	n.72C>T		non_coding_transcript_exon_variant	1/1
MIR217	unassigned_transcript_353	n.1C>T		non_coding_transcript_exon_variant	1/1
MIR217HG	NR_126406.1	n.209-19123C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000272180	ENST00000606639.1	n.82+30766G>A		intron_variant		1
MIR217	ENST00000384817.3	n.72C>T		non_coding_transcript_exon_variant	1/1	6
MIR217HG	ENST00000446139.1	n.209-19123C>T		intron_variant		5
MIR217HG	ENST00000701602.1	n.407+10868C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0142 AC: 2153 AN: 152150 Hom.: 25 Cov.: 32

Gnomad AFR AF: 0.00500

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0275

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00290

Gnomad FIN AF: 0.00679

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.0201

Gnomad OTH AF: 0.0230

GnomAD3 exomes AF: 0.0135 AC: 3356 AN: 247852 Hom.: 42 AF XY: 0.0135 AC XY: 1812 AN XY: 134158

Gnomad AFR exome AF: 0.00420

Gnomad AMR exome AF: 0.0162

Gnomad ASJ exome AF: 0.00511

Gnomad EAS exome AF: 0.000110

Gnomad SAS exome AF: 0.00411

Gnomad FIN exome AF: 0.00947

Gnomad NFE exome AF: 0.0202

Gnomad OTH exome AF: 0.0156

GnomAD4 exome AF: 0.0140 AC: 5338 AN: 380578 Hom.: 61 Cov.: 0 AF XY: 0.0133 AC XY: 2888 AN XY: 216602

Gnomad4 AFR exome AF: 0.00392

Gnomad4 AMR exome AF: 0.0161

Gnomad4 ASJ exome AF: 0.00496

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00420

Gnomad4 FIN exome AF: 0.0101

Gnomad4 NFE exome AF: 0.0198

Gnomad4 OTH exome AF: 0.0140

GnomAD4 genome AF: 0.0141 AC: 2152 AN: 152268 Hom.: 25 Cov.: 32 AF XY: 0.0132 AC XY: 985 AN XY: 74458

Gnomad4 AFR AF: 0.00498

Gnomad4 AMR AF: 0.0275

Gnomad4 ASJ AF: 0.00490

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00291

Gnomad4 FIN AF: 0.00679

Gnomad4 NFE AF: 0.0201

Gnomad4 OTH AF: 0.0227

Alfa AF: 0.0137 Hom.: 4

Bravo AF: 0.0146

Asia WGS AF: 0.00173 AC: 6 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.18
CADD	Benign	19
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41291173; hg19: chr2-56210140;