18-5762619-G-A

Variant names:

• chr18-5762619-G-A
• rs11662748
• ENST00000566533.6:n.331+146G>A

Variant summary

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

The ENST00000566533.6(MIR3976HG):​n.331+146G>A variant causes a intron 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 ENST00000566533.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000566533.6. 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_038839.1		n.322+146G>A		intron	N/A
	MIR3976HG	NR_172494.1		n.342+146G>A		intron	N/A
	MIR3976HG	NR_172495.1		n.342+146G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3976HG	ENST00000566533.6	TSL:1	n.331+146G>A		intron	N/A
	MIR3976HG	ENST00000668692.1		n.478G>A		splice_region non_coding_transcript_exon	Exon 2 of 5
	MIR3976HG	ENST00000763411.1		n.462G>A		non_coding_transcript_exon	Exon 2 of 2

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

African (AFR) AF: 0.167 AC: 1 AN: 6

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.125 AC: 1 AN: 8

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.313 AC: 10 AN: 32

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.200 AC: 20 AN: 100

Other (OTH) AF: 0.167 AC: 1 AN: 6

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

African (AFR) AF: 0.0528 AC: 2192 AN: 41542

American (AMR) AF: 0.149 AC: 2279 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 679 AN: 3470

East Asian (EAS) AF: 0.118 AC: 609 AN: 5172

South Asian (SAS) AF: 0.181 AC: 872 AN: 4818

European-Finnish (FIN) AF: 0.268 AC: 2836 AN: 10586

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.239 AC: 16248 AN: 68014

Other (OTH) AF: 0.173 AC: 366 AN: 2114

Alfa AF: 0.196 Hom.: 5023

Bravo AF: 0.157

Asia WGS AF: 0.146 AC: 512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.6
DANN	Benign	0.68
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs11662748; hg19: chr18-5762618;