rs4798405

chr18-5742207-A-Gchr18-5742207-A-T

Variant summary

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

The ENST00000654302.1(MIR3976HG):n.242-953A>G 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 0.612 in 152,096 control chromosomes in the GnomAD database, including 30,013 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 0.61 (30013 hom., cov: 33)
• Consequence: MIR3976HG ENST00000654302.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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 = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR3976HG	ENST00000654302.1	n.242-953A>G		intron_variant, non_coding_transcript_variant
MIR3976HG	ENST00000656406.1	n.897-958A>G		intron_variant, non_coding_transcript_variant
MIR3976HG	ENST00000661123.1	n.1876-953A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92954 AN: 151978 Hom.: 29951 Cov.: 33

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.612 AC: 93082 AN: 152096 Hom.: 30013 Cov.: 33 AF XY: 0.610 AC XY: 45358 AN XY: 74360

Gnomad4 AFR AF: 0.826

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.598

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.573

Alfa AF: 0.536 Hom.: 28659

Bravo AF: 0.633

Asia WGS AF: 0.598 AC: 2082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.7
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4798405; hg19: chr18-5742206;