rs2577256

Variant names:

• chr2-11832364-T-C
• rs2577256
• XR_922803.3:n.143T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-11832364-T-C
• chr2-11832364-T-G

Variant summary

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

The XR_922803.3(LOC105373430):​n.143T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 151,816 control chromosomes in the GnomAD database, including 21,318 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 0.51 (21318 hom., cov: 30)
• Consequence: LOC105373430 XR_922803.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119
• Publications: 6 publications found

Genes affected

LOC105373430 (HGNC:):

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000842235.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3681HG	ENST00000842235.1		n.204-237T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78041 AN: 151698 Hom.: 21274 Cov.: 30

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.515 AC: 78125 AN: 151816 Hom.: 21318 Cov.: 30 AF XY: 0.506 AC XY: 37556 AN XY: 74190

African (AFR) AF: 0.674 AC: 27857 AN: 41340

American (AMR) AF: 0.428 AC: 6534 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1844 AN: 3472

East Asian (EAS) AF: 0.174 AC: 898 AN: 5148

South Asian (SAS) AF: 0.286 AC: 1376 AN: 4808

European-Finnish (FIN) AF: 0.446 AC: 4696 AN: 10526

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33227 AN: 67930

Other (OTH) AF: 0.491 AC: 1036 AN: 2108

Alfa AF: 0.501 Hom.: 25720

Bravo AF: 0.522

Asia WGS AF: 0.269 AC: 941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.1
DANN	Benign	0.55
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs2577256; hg19: chr2-11972490;