rs11696896

chr20-60222868-G-A

Variant summary

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

The NR_046099.1(MIR646HG):n.332+41955G>A 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 0.091 in 152,186 control chromosomes in the GnomAD database, including 743 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 0.091 (743 hom., cov: 32)
• Consequence: MIR646HG NR_046099.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR646HG	NR_046099.1	n.332+41955G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR646HG	ENST00000659856.1	n.353+41955G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0910 AC: 13842 AN: 152068 Hom.: 744 Cov.: 32

Gnomad AFR AF: 0.0830

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.0505

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0728

Gnomad OTH AF: 0.0945

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

GnomAD4 genome AF: 0.0910 AC: 13855 AN: 152186 Hom.: 743 Cov.: 32 AF XY: 0.0952 AC XY: 7087 AN XY: 74408

Gnomad4 AFR AF: 0.0828

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.0505

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.0728

Gnomad4 OTH AF: 0.0973

Alfa AF: 0.0931 Hom.: 125

Bravo AF: 0.0931

Asia WGS AF: 0.146 AC: 507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.7
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11696896; hg19: chr20-58797926;