rs7940296

Variant names:

• chr11-82684742-A-G
• rs7940296
• ENST00000532217.1:n.345-11555T>C

Your query was ambiguous. Multiple possible variants found:

• chr11-82684742-A-G
• chr11-82684742-A-T

Variant summary

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

The ENST00000532217.1(MIR4300HG):​n.345-11555T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 152,086 control chromosomes in the GnomAD database, including 21,270 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 0.52 (21270 hom., cov: 32)
• Consequence: MIR4300HG ENST00000532217.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.366
• Publications: 2 publications found

Genes affected

MIR4300HG (HGNC:52003): (MIR4300 host gene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000532217.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4300HG	ENST00000532217.1	TSL:5	n.345-11555T>C		intron	N/A
	MIR4300HG	ENST00000671287.1		n.769-11555T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78713 AN: 151966 Hom.: 21231 Cov.: 32

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.518 AC: 78808 AN: 152086 Hom.: 21270 Cov.: 32 AF XY: 0.520 AC XY: 38663 AN XY: 74344

African (AFR) AF: 0.645 AC: 26756 AN: 41470

American (AMR) AF: 0.584 AC: 8924 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1509 AN: 3468

East Asian (EAS) AF: 0.668 AC: 3461 AN: 5182

South Asian (SAS) AF: 0.585 AC: 2821 AN: 4820

European-Finnish (FIN) AF: 0.395 AC: 4170 AN: 10568

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29621 AN: 67990

Other (OTH) AF: 0.518 AC: 1093 AN: 2112

Alfa AF: 0.467 Hom.: 54996

Bravo AF: 0.539

Asia WGS AF: 0.637 AC: 2216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.4
DANN	Benign	0.63
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs7940296; hg19: chr11-82395784;