1-98037378-G-T

Position:

• chr1-98037378-G-T

Variant summary

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

The NR_046105.1(MIR137HG):​n.814+8630C>A variant causes a intron, non coding transcript 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 NR_046105.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.328

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR137HG	NR_046105.1	n.814+8630C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR137HG	ENST00000602672.2	n.140+8630C>A		intron_variant, non_coding_transcript_variant		5
MIR137HG	ENST00000424528.2	n.984+8630C>A		intron_variant, non_coding_transcript_variant		2
MIR137HG	ENST00000634594.1	n.756+7172C>A		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.696

Gnomad4 AMR AF: 0.865

Gnomad4 ASJ AF: 0.889

Gnomad4 EAS AF: 0.940

Gnomad4 SAS AF: 0.800

Gnomad4 FIN AF: 0.737

Gnomad4 NFE AF: 0.804

Gnomad4 OTH AF: 0.800

Alfa AF: 0.810 Hom.: 73735

Bravo AF: 0.790

Asia WGS AF: 0.852 AC: 2937 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1625579; hg19: chr1-98502934;