rs531564

Positions:

• chr8-9903189-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000519461.2(MIR124-1HG):​n.210C>G 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 0.124 in 352,428 control chromosomes in the GnomAD database, including 2,940 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 0.13 (1486 hom., cov: 33)
  • Exomes 𝑓: 0.12 (1454 hom.)
• Consequence: MIR124-1HG ENST00000519461.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370

Genes affected

MIR124-1HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR124-1HG	NR_024281.1	n.141C>G		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR124-1HG	ENST00000519461.2	n.210C>G		non_coding_transcript_exon_variant	1/3	1
MIR124-1HG	ENST00000517675.1	n.209C>G		non_coding_transcript_exon_variant	1/1	6
MIR124-1HG	ENST00000521863.1	n.523C>G		non_coding_transcript_exon_variant	3/3	5

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20522 AN: 152066 Hom.: 1479 Cov.: 33

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0818

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.0675

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.122

GnomAD4 exome AF: 0.115 AC: 23052 AN: 200244 Hom.: 1454 Cov.: 0 AF XY: 0.109 AC XY: 12057 AN XY: 110902

Gnomad4 AFR exome AF: 0.168

Gnomad4 AMR exome AF: 0.0842

Gnomad4 ASJ exome AF: 0.0869

Gnomad4 EAS exome AF: 0.148

Gnomad4 SAS exome AF: 0.0673

Gnomad4 FIN exome AF: 0.149

Gnomad4 NFE exome AF: 0.130

Gnomad4 OTH exome AF: 0.121

GnomAD4 genome AF: 0.135 AC: 20541 AN: 152184 Hom.: 1486 Cov.: 33 AF XY: 0.133 AC XY: 9871 AN XY: 74396

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.0818

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.0665

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.121

Alfa AF: 0.131 Hom.: 164

Bravo AF: 0.132

Asia WGS AF: 0.0900 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	12
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs531564; hg19: chr8-9760699; COSMIC: COSV66118674;