XR_007067681.1:n.5326C>A

Variant names:

• chr20-60479457-C-A
• rs348790
• XR_007067681.1:n.5326C>A

Variant summary

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

The XR_007067681.1(LOC124904944):​n.5326C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 152,110 control chromosomes in the GnomAD database, including 20,784 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 0.51 (20784 hom., cov: 33)
• Consequence: LOC124904944 XR_007067681.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 3 publications found

Genes affected

LOC124904944 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 = 0.762 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000437035.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR646HG	ENST00000437035.5	TSL:5	n.428-47930C>A		intron	N/A
	MIR646HG	ENST00000659856.1		n.354-47930C>A		intron	N/A
	MIR646HG	ENST00000665114.1		n.359-47930C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.507 AC: 77009 AN: 151994 Hom.: 20784 Cov.: 33

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.506 AC: 77025 AN: 152110 Hom.: 20784 Cov.: 33 AF XY: 0.510 AC XY: 37892 AN XY: 74352

African (AFR) AF: 0.311 AC: 12887 AN: 41496

American (AMR) AF: 0.531 AC: 8120 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1682 AN: 3470

East Asian (EAS) AF: 0.782 AC: 4041 AN: 5166

South Asian (SAS) AF: 0.569 AC: 2742 AN: 4822

European-Finnish (FIN) AF: 0.604 AC: 6390 AN: 10572

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.579 AC: 39347 AN: 67982

Other (OTH) AF: 0.516 AC: 1089 AN: 2112

Alfa AF: 0.546 Hom.: 27194

Bravo AF: 0.496

Asia WGS AF: 0.656 AC: 2280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.71
PhyloP100		-0.097

Splicing

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

Other links and lift over

dbSNP: rs348790; hg19: chr20-59054515;