10-21494705-G-T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NR_160800.1(MIR1915HG):​n.1752C>A 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 0.0000511 in 19,586 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 34)
  • Exomes 𝑓: 0.000051 (0 hom.)
• Consequence: MIR1915HG NR_160800.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• Publications: 0 publications found

Genes affected

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

ENSG00000308071 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_160800.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR1915HG	NR_160800.1		n.1752C>A		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR1915HG	ENST00000658000.1		n.1752C>A		non_coding_transcript_exon	Exon 2 of 2
	MIR1915HG	ENST00000701218.2		n.322+2045C>A		intron	N/A
	MIR1915HG	ENST00000830463.1		n.259+2045C>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome AF: 0.0000511 AC: 1 AN: 19586 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 10266

African (AFR) AF: 0.00 AC: 0 AN: 404

American (AMR) AF: 0.00 AC: 0 AN: 394

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 500

East Asian (EAS) AF: 0.00 AC: 0 AN: 2340

South Asian (SAS) AF: 0.00 AC: 0 AN: 136

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2822

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 62

European-Non Finnish (NFE) AF: 0.0000839 AC: 1 AN: 11920

Other (OTH) AF: 0.00 AC: 0 AN: 1008

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	13
DANN	Benign	0.89
PhyloP100		-0.0070
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

Other links and lift over

dbSNP: rs12770228; hg19: chr10-21783634;