rs11907714

chr20-60221559-A-G

Variant summary

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

The NR_046099.1(MIR646HG):n.332+40646A>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 0.195 in 152,202 control chromosomes in the GnomAD database, including 4,664 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 0.20 (4664 hom., cov: 33)
• Consequence: MIR646HG NR_046099.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386

Genes affected

MIR646HG (HGNC:27659): (MIR646 host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR646HG	NR_046099.1	n.332+40646A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR646HG	ENST00000659856.1	n.353+40646A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29681 AN: 152084 Hom.: 4638 Cov.: 33

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.0571

Gnomad SAS AF: 0.0985

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0907

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.195 AC: 29755 AN: 152202 Hom.: 4664 Cov.: 33 AF XY: 0.196 AC XY: 14597 AN XY: 74426

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.0572

Gnomad4 SAS AF: 0.0988

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.0907

Gnomad4 OTH AF: 0.168

Alfa AF: 0.106 Hom.: 1684

Bravo AF: 0.203

Asia WGS AF: 0.121 AC: 420 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	0.56
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11907714; hg19: chr20-58796617;