8-9918006-T-C

Variant names:

• chr8-9918006-T-C
• rs473034
• ENST00000693527.2:n.105+1049A>G

Variant summary

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

The ENST00000693527.2(MIR124-1HG):​n.105+1049A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.854 in 152,196 control chromosomes in the GnomAD database, including 55,489 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 0.85 (55489 hom., cov: 33)
• Consequence: MIR124-1HG ENST00000693527.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338
• Publications: 7 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.869 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR124-1HG	ENST00000693527.2		n.105+1049A>G		intron	N/A
	MIR124-1HG	ENST00000700799.2		n.124+1049A>G		intron	N/A
	MIR124-1HG	ENST00000701445.2		n.179+1049A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.854 AC: 129829 AN: 152078 Hom.: 55465 Cov.: 33

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.894

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.920

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.854 AC: 129904 AN: 152196 Hom.: 55489 Cov.: 33 AF XY: 0.852 AC XY: 63373 AN XY: 74406

African (AFR) AF: 0.830 AC: 34469 AN: 41512

American (AMR) AF: 0.852 AC: 13028 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.920 AC: 3193 AN: 3472

East Asian (EAS) AF: 0.812 AC: 4195 AN: 5166

South Asian (SAS) AF: 0.865 AC: 4176 AN: 4830

European-Finnish (FIN) AF: 0.801 AC: 8480 AN: 10582

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.874 AC: 59481 AN: 68020

Other (OTH) AF: 0.853 AC: 1805 AN: 2116

Alfa AF: 0.868 Hom.: 79858

Bravo AF: 0.852

Asia WGS AF: 0.803 AC: 2795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.48
DANN	Benign	0.73
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs473034; hg19: chr8-9775516;