chr11-82701071-T-C

Variant names:

• chr11-82701071-T-C
• rs10501536
• ENST00000532217.1:n.344+11998A>G

Variant summary

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

The ENST00000532217.1(MIR4300HG):​n.344+11998A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0415 in 152,192 control chromosomes in the GnomAD database, including 180 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 0.042 (180 hom., cov: 32)
• Consequence: MIR4300HG ENST00000532217.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.435
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0915 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.344+11998A>G		intron_variant	Intron 2 of 4	5
MIR4300HG	ENST00000671287.1	n.768+11998A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0415 AC: 6311 AN: 152074 Hom.: 180 Cov.: 32

Gnomad AFR AF: 0.0644

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0511

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.0992

Gnomad SAS AF: 0.0359

Gnomad FIN AF: 0.0817

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0174

Gnomad OTH AF: 0.0321

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

GnomAD4 genome AF: 0.0415 AC: 6319 AN: 152192 Hom.: 180 Cov.: 32 AF XY: 0.0464 AC XY: 3449 AN XY: 74404

African (AFR) AF: 0.0644 AC: 2673 AN: 41526

American (AMR) AF: 0.0511 AC: 781 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0164 AC: 57 AN: 3472

East Asian (EAS) AF: 0.0986 AC: 510 AN: 5172

South Asian (SAS) AF: 0.0368 AC: 177 AN: 4816

European-Finnish (FIN) AF: 0.0817 AC: 865 AN: 10586

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0174 AC: 1182 AN: 68014

Other (OTH) AF: 0.0323 AC: 68 AN: 2108

Alfa AF: 0.0229 Hom.: 122

Bravo AF: 0.0400

Asia WGS AF: 0.0770 AC: 266 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	0.99
DANN	Benign	0.73
PhyloP100		-0.43
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10501536; hg19: chr11-82412113;