rs77177281

chr1-98006146-A-Gchr1-98006146-A-T

Variant summary

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

The NR_046105.1(MIR137HG):n.815-11146T>C 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 0.0247 in 152,158 control chromosomes in the GnomAD database, including 107 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 0.025 (107 hom., cov: 32)
• Consequence: MIR137HG NR_046105.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR137HG	NR_046105.1	n.815-11146T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR137HG	ENST00000602672.2	n.141-26831T>C		intron_variant, non_coding_transcript_variant		5
MIR137HG	ENST00000424528.2	n.985-11146T>C		intron_variant, non_coding_transcript_variant		2
MIR137HG	ENST00000634594.1	n.757-16577T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0248 AC: 3764 AN: 152040 Hom.: 107 Cov.: 32

Gnomad AFR AF: 0.00408

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0158

Gnomad ASJ AF: 0.00980

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0592

Gnomad FIN AF: 0.0916

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0294

Gnomad OTH AF: 0.0273

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

GnomAD4 genome AF: 0.0247 AC: 3763 AN: 152158 Hom.: 107 Cov.: 32 AF XY: 0.0273 AC XY: 2032 AN XY: 74400

Gnomad4 AFR AF: 0.00407

Gnomad4 AMR AF: 0.0158

Gnomad4 ASJ AF: 0.00980

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0595

Gnomad4 FIN AF: 0.0916

Gnomad4 NFE AF: 0.0294

Gnomad4 OTH AF: 0.0270

Alfa AF: 0.0168 Hom.: 8

Bravo AF: 0.0169

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	2.5
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs77177281; hg19: chr1-98471702;