rs2175961

chr11-82330805-T-C

Variant summary

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

The NR_120571.1(MIR4300HG):n.431+19121A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,098 control chromosomes in the GnomAD database, including 1,307 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 0.12 (1307 hom., cov: 33)
• Consequence: MIR4300HG NR_120571.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR4300HG	NR_120571.1	n.431+19121A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR4300HG	ENST00000532217.1	n.557+25707A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18513 AN: 151980 Hom.: 1304 Cov.: 33

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0992

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0412

Gnomad FIN AF: 0.0573

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.122 AC: 18531 AN: 152098 Hom.: 1307 Cov.: 33 AF XY: 0.119 AC XY: 8852 AN XY: 74360

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.0992

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0408

Gnomad4 FIN AF: 0.0573

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.129

Alfa AF: 0.119 Hom.: 140

Bravo AF: 0.129

Asia WGS AF: 0.0330 AC: 117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.3
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2175961; hg19: chr11-82041847;