18-5753005-C-T

Position:

• chr18-5753005-C-T

Variant summary

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

The NR_172496.1(MIR3976HG):​n.166+4041C>T 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 0.609 in 152,058 control chromosomes in the GnomAD database, including 29,064 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 (29064 hom., cov: 32)
• Consequence: MIR3976HG NR_172496.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.83

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR3976HG	NR_172496.1	n.166+4041C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR3976HG	ENST00000562452.2	n.146+4041C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92521 AN: 151940 Hom.: 29032 Cov.: 32

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.609 AC: 92611 AN: 152058 Hom.: 29064 Cov.: 32 AF XY: 0.612 AC XY: 45508 AN XY: 74328

Gnomad4 AFR AF: 0.752

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.583

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.522

Gnomad4 OTH AF: 0.589

Alfa AF: 0.544 Hom.: 21226

Bravo AF: 0.618

Asia WGS AF: 0.691 AC: 2396 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1917917; hg19: chr18-5753004;