rs77177281

Variant names:

• chr1-98006146-A-G
• rs77177281
• ENST00000424528.2:n.985-11146T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-98006146-A-G
• chr1-98006146-A-T

Variant summary

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

The ENST00000424528.2(MIR137HG):​n.985-11146T>C variant causes a intron 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 ENST00000424528.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 1 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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0538 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000424528.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR137HG	NR_046105.1		n.815-11146T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR137HG	ENST00000424528.2	TSL:2	n.985-11146T>C		intron	N/A
	MIR137HG	ENST00000602672.2	TSL:5	n.141-26831T>C		intron	N/A
	MIR137HG	ENST00000634594.2	TSL:5	n.773-16577T>C		intron	N/A

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

African (AFR) AF: 0.00407 AC: 169 AN: 41544

American (AMR) AF: 0.0158 AC: 241 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.00980 AC: 34 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5180

South Asian (SAS) AF: 0.0595 AC: 287 AN: 4826

European-Finnish (FIN) AF: 0.0916 AC: 971 AN: 10604

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0294 AC: 1995 AN: 67972

Other (OTH) AF: 0.0270 AC: 57 AN: 2110

Alfa AF: 0.0199 Hom.: 18

Bravo AF: 0.0169

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.86
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs77177281; hg19: chr1-98471702;