1-98046571-G-A

Variant names:

• chr1-98046571-G-A
• rs2660304
• ENST00000602852.3:n.673C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000602852.3(MIR137HG):​n.673C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 28)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MIR137HG ENST00000602852.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 43 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR137HG	NR_046105.1	n.373C>T		non_coding_transcript_exon_variant	Exon 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR137HG	ENST00000602852.3	n.673C>T		non_coding_transcript_exon_variant	Exon 2 of 4	1
MIR137HG	ENST00000424528.2	n.543C>T		non_coding_transcript_exon_variant	Exon 2 of 5	2
MIR137HG	ENST00000687457.2	n.551C>T		non_coding_transcript_exon_variant	Exon 2 of 3

Frequencies

GnomAD3 genomes Cov.: 28

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 21272 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 11488

African (AFR) AF: 0.00 AC: 0 AN: 498

American (AMR) AF: 0.00 AC: 0 AN: 2356

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 360

East Asian (EAS) AF: 0.00 AC: 0 AN: 1272

South Asian (SAS) AF: 0.00 AC: 0 AN: 2828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 492

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 68

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 12368

Other (OTH) AF: 0.00 AC: 0 AN: 1030

GnomAD4 genome Cov.: 28

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	17
DANN	Benign	0.83
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs2660304; hg19: chr1-98512127;