chr1-98046571-G-T

Position:

• chr1-98046571-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.373C>A 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 0.826 in 172,920 control chromosomes in the GnomAD database, including 59,270 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 0.83 (52049 hom., cov: 28)
  • Exomes 𝑓: 0.82 (7221 hom.)
• Consequence: MIR137HG NR_046105.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26

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=-0.7).
• 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	UniProt
MIR137HG	NR_046105.1	n.373C>A		non_coding_transcript_exon_variant	2/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR137HG	ENST00000424528.2	n.543C>A		non_coding_transcript_exon_variant	2/5	2
MIR137HG	ENST00000687457.2	n.551C>A		non_coding_transcript_exon_variant	2/3

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125317 AN: 151590 Hom.: 52012 Cov.: 28

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.876

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.827

GnomAD4 exome AF: 0.819 AC: 17379 AN: 21212 Hom.: 7221 Cov.: 0 AF XY: 0.818 AC XY: 9367 AN XY: 11454

Gnomad4 AFR exome AF: 0.881

Gnomad4 AMR exome AF: 0.901

Gnomad4 ASJ exome AF: 0.894

Gnomad4 EAS exome AF: 0.946

Gnomad4 SAS exome AF: 0.801

Gnomad4 FIN exome AF: 0.722

Gnomad4 NFE exome AF: 0.794

Gnomad4 OTH exome AF: 0.816

GnomAD4 genome AF: 0.827 AC: 125411 AN: 151708 Hom.: 52049 Cov.: 28 AF XY: 0.826 AC XY: 61198 AN XY: 74088

Gnomad4 AFR AF: 0.852

Gnomad4 AMR AF: 0.877

Gnomad4 ASJ AF: 0.889

Gnomad4 EAS AF: 0.940

Gnomad4 SAS AF: 0.801

Gnomad4 FIN AF: 0.737

Gnomad4 NFE AF: 0.804

Gnomad4 OTH AF: 0.828

Alfa AF: 0.813 Hom.: 6279

Bravo AF: 0.840

Asia WGS AF: 0.868 AC: 3021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	17
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2660304; hg19: chr1-98512127;