1-98037378-G-T

Variant names:

• chr1-98037378-G-T
• rs1625579
• ENST00000424528.2:n.984+8630C>A

Variant summary

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

The ENST00000424528.2(MIR137HG):​n.984+8630C>A 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 151,826 control chromosomes in the GnomAD database, including 46,917 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 (46917 hom., cov: 31)
• Consequence: MIR137HG ENST00000424528.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.328
• Publications: 187 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR137HG	NR_046105.1		n.814+8630C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR137HG	ENST00000424528.2	TSL:2	n.984+8630C>A		intron	N/A
	MIR137HG	ENST00000602672.2	TSL:5	n.140+8630C>A		intron	N/A
	MIR137HG	ENST00000634594.2	TSL:5	n.772+7172C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.783 AC: 118747 AN: 151708 Hom.: 46893 Cov.: 31

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.815

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.783 AC: 118809 AN: 151826 Hom.: 46917 Cov.: 31 AF XY: 0.783 AC XY: 58129 AN XY: 74220

African (AFR) AF: 0.696 AC: 28844 AN: 41428

American (AMR) AF: 0.865 AC: 13178 AN: 15234

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

East Asian (EAS) AF: 0.940 AC: 4849 AN: 5160

South Asian (SAS) AF: 0.800 AC: 3857 AN: 4820

European-Finnish (FIN) AF: 0.737 AC: 7793 AN: 10574

Middle Eastern (MID) AF: 0.822 AC: 240 AN: 292

European-Non Finnish (NFE) AF: 0.804 AC: 54534 AN: 67834

Other (OTH) AF: 0.800 AC: 1688 AN: 2110

Alfa AF: 0.804 Hom.: 159165

Bravo AF: 0.790

Asia WGS AF: 0.852 AC: 2937 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.50
PhyloP100		-0.33

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1625579;

hg19: chr1-98502934;