rs10495593

Variant names:

• chr2-12189221-G-T
• rs10495593
• ENST00000412294.6:n.325+22366G>T

Variant summary

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

The ENST00000412294.6(MIR3681HG):​n.325+22366G>T variant causes a intron 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 ENST00000412294.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.620
• Publications: 5 publications found

Genes affected

MIR3681HG (HGNC:52001): (MIR3681 host gene)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MIR3681HG	NR_110196.1	n.327+22366G>T		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR3681HG	ENST00000412294.6	n.325+22366G>T		intron_variant	Intron 3 of 5	2
MIR3681HG	ENST00000438292.5	n.246+22366G>T		intron_variant	Intron 3 of 4	3
MIR3681HG	ENST00000824630.1	n.459-5359G>T		intron_variant	Intron 4 of 4

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

African (AFR) AF: 0.0375 AC: 1557 AN: 41524

American (AMR) AF: 0.235 AC: 3584 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0648 AC: 225 AN: 3470

East Asian (EAS) AF: 0.458 AC: 2361 AN: 5152

South Asian (SAS) AF: 0.400 AC: 1926 AN: 4820

European-Finnish (FIN) AF: 0.0805 AC: 853 AN: 10600

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0908 AC: 6175 AN: 67992

Other (OTH) AF: 0.123 AC: 260 AN: 2108

Alfa AF: 0.0875 Hom.: 114

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
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs10495593; hg19: chr2-12329347;