2-12059092-T-C

Position:

• chr2-12059092-T-C

Variant summary

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

The NR_110196.1(MIR3681HG):​n.209+51249T>C 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 0.758 in 152,164 control chromosomes in the GnomAD database, including 43,936 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 0.76 (43936 hom., cov: 32)
• Consequence: MIR3681HG NR_110196.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.903

Genes affected

MIR3681HG (HGNC:52001): (MIR3681 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 (EAS) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR3681HG	NR_110196.1	n.209+51249T>C		intron_variant, non_coding_transcript_variant
MIR3681HG	NR_110197.1	n.210-47726T>C		intron_variant, non_coding_transcript_variant
MIR3681HG	NR_110198.1	n.210-24357T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR3681HG	ENST00000412294.5	n.197+51249T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.758 AC: 115243 AN: 152046 Hom.: 43878 Cov.: 32

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.758 AC: 115360 AN: 152164 Hom.: 43936 Cov.: 32 AF XY: 0.760 AC XY: 56579 AN XY: 74408

Gnomad4 AFR AF: 0.707

Gnomad4 AMR AF: 0.824

Gnomad4 ASJ AF: 0.773

Gnomad4 EAS AF: 0.871

Gnomad4 SAS AF: 0.833

Gnomad4 FIN AF: 0.722

Gnomad4 NFE AF: 0.765

Gnomad4 OTH AF: 0.777

Alfa AF: 0.750 Hom.: 8386

Bravo AF: 0.762

Asia WGS AF: 0.867 AC: 3016 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.15
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7562854; hg19: chr2-12199218;