chr2-11897053-C-T

Variant names:

• chr2-11897053-C-T
• rs17605562
• ENST00000438292.5:n.31+31138C>T

Variant summary

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

The ENST00000438292.5(MIR3681HG):​n.31+31138C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0336 in 152,260 control chromosomes in the GnomAD database, including 111 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 0.034 (111 hom., cov: 33)
• Consequence: MIR3681HG ENST00000438292.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.607

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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR3681HG	ENST00000438292.5	n.31+31138C>T		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.0336 AC: 5117 AN: 152142 Hom.: 111 Cov.: 33

Gnomad AFR AF: 0.00758

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0261

Gnomad ASJ AF: 0.0597

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0728

Gnomad FIN AF: 0.0412

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0482

Gnomad OTH AF: 0.0383

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

GnomAD4 genome AF: 0.0336 AC: 5117 AN: 152260 Hom.: 111 Cov.: 33 AF XY: 0.0335 AC XY: 2494 AN XY: 74450

Gnomad4 AFR AF: 0.00758

Gnomad4 AMR AF: 0.0261

Gnomad4 ASJ AF: 0.0597

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0729

Gnomad4 FIN AF: 0.0412

Gnomad4 NFE AF: 0.0482

Gnomad4 OTH AF: 0.0379

Alfa AF: 0.0438 Hom.: 200

Bravo AF: 0.0291

Asia WGS AF: 0.0270 AC: 94 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.30
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: rs17605562; hg19: chr2-12037179;