rs10495593

chr2-12189221-G-T

Variant summary

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

The NR_110196.1(MIR3681HG):n.327+22366G>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 0.112 in 152,146 control chromosomes in the GnomAD database, including 1,819 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 (1819 hom., cov: 32)
• Consequence: MIR3681HG NR_110196.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.620

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR3681HG	NR_110196.1	n.327+22366G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR3681HG	ENST00000412294.5	n.315+22366G>T		intron_variant, non_coding_transcript_variant		2
MIR3681HG	ENST00000438292.5	n.246+22366G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.112 AC: 16972 AN: 152028 Hom.: 1813 Cov.: 32

Gnomad AFR AF: 0.0375

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.0648

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.0805

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0908

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.112 AC: 16991 AN: 152146 Hom.: 1819 Cov.: 32 AF XY: 0.122 AC XY: 9082 AN XY: 74394

Gnomad4 AFR AF: 0.0375

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.0648

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.0805

Gnomad4 NFE AF: 0.0908

Gnomad4 OTH AF: 0.123

Alfa AF: 0.0898 Hom.: 113

Bravo AF: 0.118

Asia WGS AF: 0.415 AC: 1444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.35
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495593; hg19: chr2-12329347;