rs1782810

Variant names:

• chr1-98036784-G-A
• rs1782810
• ENST00000424528.2:n.984+9224C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-98036784-G-A
• chr1-98036784-G-C
• chr1-98036784-G-T

Variant summary

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

The ENST00000424528.2(MIR137HG):​n.984+9224C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 151,918 control chromosomes in the GnomAD database, including 46,981 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 0.78 (46981 hom., cov: 32)
• Consequence: MIR137HG ENST00000424528.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240
• Publications: 9 publications found

Genes affected

MIR137HG (HGNC:42871): (MIR137 host gene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000424528.2. 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
	MIR137HG	NR_046105.1		n.814+9224C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR137HG	ENST00000424528.2	TSL:2	n.984+9224C>T		intron	N/A
	MIR137HG	ENST00000602672.2	TSL:5	n.140+9224C>T		intron	N/A
	MIR137HG	ENST00000634594.2	TSL:5	n.772+7766C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.783 AC: 118865 AN: 151800 Hom.: 46957 Cov.: 32

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.823

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.783 AC: 118928 AN: 151918 Hom.: 46981 Cov.: 32 AF XY: 0.784 AC XY: 58210 AN XY: 74286

African (AFR) AF: 0.697 AC: 28885 AN: 41414

American (AMR) AF: 0.865 AC: 13197 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.889 AC: 3081 AN: 3466

East Asian (EAS) AF: 0.940 AC: 4856 AN: 5168

South Asian (SAS) AF: 0.799 AC: 3854 AN: 4824

European-Finnish (FIN) AF: 0.737 AC: 7800 AN: 10578

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.804 AC: 54577 AN: 67896

Other (OTH) AF: 0.799 AC: 1687 AN: 2112

Alfa AF: 0.808 Hom.: 62366

Bravo AF: 0.790

Asia WGS AF: 0.853 AC: 2969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.32
PhyloP100		-0.024

Splicing

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

Other links and lift over

dbSNP: rs1782810; hg19: chr1-98502340;