rs12770228

chr10-21494705-G-A

Variant summary

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

The NR_160800.1(MIR1915HG):n.1752C>T 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 0.245 in 171,796 control chromosomes in the GnomAD database, including 6,346 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 0.24 (5559 hom., cov: 34)
  • Exomes 𝑓: 0.27 (787 hom.)
• Consequence: MIR1915HG NR_160800.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

Genes affected

MIR1915HG (HGNC:31448): (MIR1915 host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR1915HG	NR_160800.1	n.1752C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR1915HG	ENST00000701218.1	n.322+2045C>T		intron_variant, non_coding_transcript_variant
MIR1915HG	ENST00000658000.1	n.1752C>T		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36930 AN: 152168 Hom.: 5559 Cov.: 34

Gnomad AFR AF: 0.0964

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.00635

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.290

GnomAD4 exome AF: 0.266 AC: 5185 AN: 19510 Hom.: 787 Cov.: 0 AF XY: 0.271 AC XY: 2771 AN XY: 10236

Gnomad4 AFR exome AF: 0.101

Gnomad4 AMR exome AF: 0.201

Gnomad4 ASJ exome AF: 0.330

Gnomad4 EAS exome AF: 0.00684

Gnomad4 SAS exome AF: 0.254

Gnomad4 FIN exome AF: 0.296

Gnomad4 NFE exome AF: 0.315

Gnomad4 OTH exome AF: 0.256

GnomAD4 genome AF: 0.242 AC: 36927 AN: 152286 Hom.: 5559 Cov.: 34 AF XY: 0.244 AC XY: 18133 AN XY: 74464

Gnomad4 AFR AF: 0.0961

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.00636

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.294

Alfa AF: 0.322 Hom.: 10222

Bravo AF: 0.227

Asia WGS AF: 0.141 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
Cadd	Benign	13
Dann	Benign	0.94
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs12770228; hg19: chr10-21783634;