rs11662748

chr18-5762619-G-A

Variant summary

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

The NR_172496.1(MIR3976HG):n.342+146G>A 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 0.173 in 152,358 control chromosomes in the GnomAD database, including 2,861 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 0.17 (2858 hom., cov: 32)
  • Exomes 𝑓: 0.22 (3 hom.)
• Consequence: MIR3976HG NR_172496.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR3976HG	NR_172496.1	n.342+146G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR3976HG	ENST00000562452.2	n.322+146G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26386 AN: 152084 Hom.: 2860 Cov.: 32

Gnomad AFR AF: 0.0528

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.174

GnomAD4 exome AF: 0.224 AC: 35 AN: 156 Hom.: 3 AF XY: 0.230 AC XY: 28 AN XY: 122

Gnomad4 AFR exome AF: 0.167

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.125

Gnomad4 FIN exome AF: 0.313

Gnomad4 NFE exome AF: 0.200

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.173 AC: 26377 AN: 152202 Hom.: 2858 Cov.: 32 AF XY: 0.173 AC XY: 12846 AN XY: 74410

Gnomad4 AFR AF: 0.0528

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.173

Alfa AF: 0.220 Hom.: 3761

Bravo AF: 0.157

Asia WGS AF: 0.146 AC: 512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.6
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11662748; hg19: chr18-5762618;