8-64371134-G-T

Variant names:

• chr8-64371134-G-T
• rs190938
• ENST00000772499.1:n.104+1990G>T

Variant summary

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

The ENST00000772499.1(MIR124-2HG):​n.104+1990G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.773 in 152,158 control chromosomes in the GnomAD database, including 45,856 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 0.77 (45856 hom., cov: 33)
• Consequence: MIR124-2HG ENST00000772499.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114
• Publications: 4 publications found

Genes affected

MIR124-2HG (HGNC:48723): (MIR124-2 host gene)

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 = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR124-2HG	ENST00000772499.1	n.104+1990G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117581 AN: 152040 Hom.: 45838 Cov.: 33

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.773 AC: 117642 AN: 152158 Hom.: 45856 Cov.: 33 AF XY: 0.774 AC XY: 57586 AN XY: 74392

African (AFR) AF: 0.703 AC: 29160 AN: 41470

American (AMR) AF: 0.793 AC: 12140 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2531 AN: 3464

East Asian (EAS) AF: 0.612 AC: 3160 AN: 5160

South Asian (SAS) AF: 0.652 AC: 3144 AN: 4822

European-Finnish (FIN) AF: 0.887 AC: 9409 AN: 10602

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.816 AC: 55538 AN: 68020

Other (OTH) AF: 0.775 AC: 1637 AN: 2112

Alfa AF: 0.795 Hom.: 149019

Bravo AF: 0.764

Asia WGS AF: 0.628 AC: 2183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.7
DANN	Benign	0.52
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs190938; hg19: chr8-65283691;