18-5857092-C-T

Variant names:

• chr18-5857092-C-T
• rs11662763
• ENST00000562452.2:n.479-19161C>T

Variant summary

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

The ENST00000562452.2(MIR3976HG):​n.479-19161C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 151,856 control chromosomes in the GnomAD database, including 1,995 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 0.15 (1995 hom., cov: 32)
• Consequence: MIR3976HG ENST00000562452.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299
• Publications: 5 publications found

Genes affected

MIR3976HG (HGNC:51104): (MIR3976 host gene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000562452.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3976HG	NR_172494.1		n.603-21351C>T		intron	N/A
	MIR3976HG	NR_172495.1		n.603-19161C>T		intron	N/A
	MIR3976HG	NR_172496.1		n.603-19161C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3976HG	ENST00000562452.2	TSL:4	n.479-19161C>T		intron	N/A
	MIR3976HG	ENST00000763406.1		n.246+17582C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22820 AN: 151736 Hom.: 1990 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.0956

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0943

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.150 AC: 22854 AN: 151856 Hom.: 1995 Cov.: 32 AF XY: 0.149 AC XY: 11086 AN XY: 74166

African (AFR) AF: 0.216 AC: 8949 AN: 41372

American (AMR) AF: 0.0955 AC: 1457 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 559 AN: 3470

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5168

South Asian (SAS) AF: 0.0950 AC: 458 AN: 4820

European-Finnish (FIN) AF: 0.194 AC: 2035 AN: 10484

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8731 AN: 67972

Other (OTH) AF: 0.137 AC: 290 AN: 2112

Alfa AF: 0.132 Hom.: 3838

Bravo AF: 0.145

Asia WGS AF: 0.0540 AC: 189 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.88
DANN	Benign	0.94
PhyloP100		0.30
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11662763; hg19: chr18-5857091;