rs1880722

Positions:

• chr18-5737301-C-G
• chr18-5737301-C-T

Variant summary

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

The ENST00000654302.1(MIR3976HG):​n.242-5859C>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 0.107 in 152,174 control chromosomes in the GnomAD database, including 1,942 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 0.11 (1942 hom., cov: 33)
• Consequence: MIR3976HG ENST00000654302.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257

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 (AFR) allele frequency at 95% confidence interval = 0.286 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.242-5859C>G		intron_variant, non_coding_transcript_variant
MIR3976HG	ENST00000656406.1	n.896+2694C>G		intron_variant, non_coding_transcript_variant
MIR3976HG	ENST00000661123.1	n.911-1062C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16202 AN: 152054 Hom.: 1934 Cov.: 33

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0948

Gnomad ASJ AF: 0.0576

Gnomad EAS AF: 0.0529

Gnomad SAS AF: 0.0347

Gnomad FIN AF: 0.0219

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0243

Gnomad OTH AF: 0.0931

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

GnomAD4 genome AF: 0.107 AC: 16248 AN: 152174 Hom.: 1942 Cov.: 33 AF XY: 0.104 AC XY: 7758 AN XY: 74396

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.0950

Gnomad4 ASJ AF: 0.0576

Gnomad4 EAS AF: 0.0529

Gnomad4 SAS AF: 0.0345

Gnomad4 FIN AF: 0.0219

Gnomad4 NFE AF: 0.0243

Gnomad4 OTH AF: 0.0926

Alfa AF: 0.0741 Hom.: 151

Bravo AF: 0.123

Asia WGS AF: 0.0480 AC: 166 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	0.53
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1880722; hg19: chr18-5737300;