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. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

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
MIR4300HG	ENST00000532217.1	n.345-11555T>C		intron_variant	Intron 2 of 4	5
MIR4300HG	ENST00000671287.1	n.769-11555T>C		intron_variant	Intron 2 of 2

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

Gnomad4 AFR AF: 0.645

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.668

Gnomad4 SAS AF: 0.585

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.518

Alfa AF: 0.452 Hom.: 32583

Bravo AF: 0.539

Asia WGS AF: 0.637 AC: 2216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.4
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: rs7940296; hg19: chr11-82395784;