8-9912063-G-A

Variant names:

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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902057	XR_007061167.1	n.74-6029C>T		intron_variant	Intron 1 of 4
LOC124902057	XR_007061170.1	n.74-6701C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR124-1HG	ENST00000693527.2	n.106-6029C>T		intron_variant	Intron 1 of 5
MIR124-1HG	ENST00000700799.2	n.125-6029C>T		intron_variant	Intron 1 of 5

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 v4.3

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;