1-98046571-G-T

Variant names:

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

Variant summary

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

The ENST00000602852.3(MIR137HG):​n.673C>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 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: Benign. The variant received -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 rank	MANE	Protein	UniProt
MIR137HG	NR_046105.1	n.373C>A		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>A		non_coding_transcript_exon_variant	Exon 2 of 4	1
MIR137HG	ENST00000424528.2	n.543C>A		non_coding_transcript_exon_variant	Exon 2 of 5	2
MIR137HG	ENST00000687457.2	n.551C>A		non_coding_transcript_exon_variant	Exon 2 of 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

African (AFR) AF: 0.881 AC: 437 AN: 496

American (AMR) AF: 0.901 AC: 2120 AN: 2352

Ashkenazi Jewish (ASJ) AF: 0.894 AC: 320 AN: 358

East Asian (EAS) AF: 0.946 AC: 1203 AN: 1272

South Asian (SAS) AF: 0.801 AC: 2258 AN: 2818

European-Finnish (FIN) AF: 0.722 AC: 354 AN: 490

Middle Eastern (MID) AF: 0.809 AC: 55 AN: 68

European-Non Finnish (NFE) AF: 0.794 AC: 9795 AN: 12332

Other (OTH) AF: 0.816 AC: 837 AN: 1026

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

African (AFR) AF: 0.852 AC: 35210 AN: 41340

American (AMR) AF: 0.877 AC: 13376 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.889 AC: 3086 AN: 3470

East Asian (EAS) AF: 0.940 AC: 4827 AN: 5136

South Asian (SAS) AF: 0.801 AC: 3840 AN: 4796

European-Finnish (FIN) AF: 0.737 AC: 7729 AN: 10486

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.804 AC: 54609 AN: 67914

Other (OTH) AF: 0.828 AC: 1740 AN: 2102

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
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;