18-5753005-C-T

Variant names:

• chr18-5753005-C-T
• rs1917917
• ENST00000566533.6:n.155+4041C>T

Variant summary

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

The ENST00000566533.6(MIR3976HG):​n.155+4041C>T variant causes a intron 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 ENST00000566533.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.83
• Publications: 2 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=-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 rank	MANE	Protein	UniProt
MIR3976HG	NR_038839.1	n.146+4041C>T		intron_variant	Intron 1 of 4
MIR3976HG	NR_172494.1	n.166+4041C>T		intron_variant	Intron 1 of 8
MIR3976HG	NR_172495.1	n.166+4041C>T		intron_variant	Intron 1 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR3976HG	ENST00000566533.6	n.155+4041C>T		intron_variant	Intron 1 of 4	1
MIR3976HG	ENST00000562452.2	n.146+4041C>T		intron_variant	Intron 1 of 3	4
MIR3976HG	ENST00000580378.3	n.157+4041C>T		intron_variant	Intron 1 of 4	3

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

African (AFR) AF: 0.752 AC: 31196 AN: 41480

American (AMR) AF: 0.636 AC: 9720 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1733 AN: 3472

East Asian (EAS) AF: 0.666 AC: 3441 AN: 5170

South Asian (SAS) AF: 0.583 AC: 2808 AN: 4818

European-Finnish (FIN) AF: 0.588 AC: 6212 AN: 10570

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.522 AC: 35499 AN: 67950

Other (OTH) AF: 0.589 AC: 1245 AN: 2112

Alfa AF: 0.544 Hom.: 25482

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
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs1917917; hg19: chr18-5753004;