rs1681052

Positions:

• chr18-39553297-C-T

Variant summary

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

The NR_024391.1(MIR924HG):​n.124-17682G>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 0.0706 in 152,236 control chromosomes in the GnomAD database, including 500 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 0.071 (500 hom., cov: 32)
• Consequence: MIR924HG NR_024391.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

MIR924HG (HGNC:44332): (MIR924 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 = 0.0922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR924HG	NR_024391.1	n.124-17682G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR924HG	ENST00000670992.1	n.286-17682G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0707 AC: 10759 AN: 152118 Hom.: 501 Cov.: 32

Gnomad AFR AF: 0.0198

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.0849

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0153

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.0942

Gnomad OTH AF: 0.0923

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

GnomAD4 genome AF: 0.0706 AC: 10755 AN: 152236 Hom.: 500 Cov.: 32 AF XY: 0.0701 AC XY: 5222 AN XY: 74446

Gnomad4 AFR AF: 0.0198

Gnomad4 AMR AF: 0.0847

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0159

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.0942

Gnomad4 OTH AF: 0.0909

Alfa AF: 0.0868 Hom.: 306

Bravo AF: 0.0684

Asia WGS AF: 0.0110 AC: 37 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	0.33
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1681052; hg19: chr18-37133261;