rs12770228

Variant names:

• chr10-21494705-G-A
• rs12770228
• ENST00000658000.1:n.1752C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-21494705-G-A
• chr10-21494705-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000658000.1(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 ENST00000658000.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• Publications: 18 publications found

Genes affected

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

ENSG00000308071 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MIR1915HG	NR_160800.1	n.1752C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR1915HG	ENST00000658000.1	n.1752C>T		non_coding_transcript_exon_variant	Exon 2 of 2
MIR1915HG	ENST00000701218.2	n.322+2045C>T		intron_variant	Intron 1 of 1
MIR1915HG	ENST00000830463.1	n.259+2045C>T		intron_variant	Intron 1 of 2
ENSG00000308071	ENST00000830852.1	n.110+322G>A		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.101 AC: 41 AN: 404

American (AMR) AF: 0.201 AC: 79 AN: 394

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 165 AN: 500

East Asian (EAS) AF: 0.00684 AC: 16 AN: 2340

South Asian (SAS) AF: 0.254 AC: 34 AN: 134

European-Finnish (FIN) AF: 0.296 AC: 832 AN: 2808

Middle Eastern (MID) AF: 0.403 AC: 25 AN: 62

European-Non Finnish (NFE) AF: 0.315 AC: 3735 AN: 11862

Other (OTH) AF: 0.256 AC: 258 AN: 1006

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

African (AFR) AF: 0.0961 AC: 3997 AN: 41582

American (AMR) AF: 0.238 AC: 3649 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1276 AN: 3468

East Asian (EAS) AF: 0.00636 AC: 33 AN: 5186

South Asian (SAS) AF: 0.229 AC: 1106 AN: 4834

European-Finnish (FIN) AF: 0.339 AC: 3600 AN: 10604

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22053 AN: 67986

Other (OTH) AF: 0.294 AC: 622 AN: 2114

Alfa AF: 0.313 Hom.: 13853

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
PhyloP100		-0.0070
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12770228; hg19: chr10-21783634;