20-60479457-C-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904944	XR_007067681.1	n.5326C>A		non_coding_transcript_exon_variant	Exon 2 of 2
LOC124904944	XR_007067682.1	n.5875C>A		non_coding_transcript_exon_variant	Exon 2 of 2
LOC124904944	XR_007067683.1	n.4827C>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR646HG	ENST00000437035.5	n.428-47930C>A		intron_variant	Intron 4 of 4	5
MIR646HG	ENST00000659856.1	n.354-47930C>A		intron_variant	Intron 3 of 5
MIR646HG	ENST00000665114.1	n.359-47930C>A		intron_variant	Intron 3 of 4

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 v4.3

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;