rs516175

Variant names:

• chr8-9912063-G-A
• rs516175
• ENST00000693527.2:n.106-6029C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-9912063-G-A
• chr8-9912063-G-C

Variant summary

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

The ENST00000693527.2(MIR124-1HG):​n.106-6029C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,172 control chromosomes in the GnomAD database, including 1,914 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 0.15 (1914 hom., cov: 33)
• Consequence: MIR124-1HG ENST00000693527.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700
• Publications: 6 publications found

Genes affected

MIR124-1HG (HGNC:27231): (MIR124-1 host gene) Predicted to act upstream of or within several processes, including gene silencing by miRNA; long-term synaptic potentiation; and sensory perception of sound. [provided by Alliance of Genome Resources, Apr 2022]

LOC124902057 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000693527.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR124-1HG	ENST00000693527.2		n.106-6029C>T		intron	N/A
	MIR124-1HG	ENST00000700799.2		n.125-6029C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22745 AN: 152054 Hom.: 1899 Cov.: 33

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.0775

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.139

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.150 AC: 22804 AN: 152172 Hom.: 1914 Cov.: 33 AF XY: 0.151 AC XY: 11212 AN XY: 74408

African (AFR) AF: 0.205 AC: 8502 AN: 41502

American (AMR) AF: 0.151 AC: 2310 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0775 AC: 269 AN: 3470

East Asian (EAS) AF: 0.182 AC: 944 AN: 5180

South Asian (SAS) AF: 0.135 AC: 650 AN: 4826

European-Finnish (FIN) AF: 0.186 AC: 1970 AN: 10584

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7761 AN: 67994

Other (OTH) AF: 0.145 AC: 306 AN: 2114

Alfa AF: 0.113 Hom.: 455

Bravo AF: 0.153

Asia WGS AF: 0.198 AC: 689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.57
DANN	Benign	0.69
PhyloP100		0.070

Splicing

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

Other links and lift over

dbSNP: rs516175; hg19: chr8-9769573;