rs348790

Positions:

• chr20-60479457-C-A
• chr20-60479457-C-G
• chr20-60479457-C-T

Variant summary

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

The XR_007067682.1(LOC124904944):​n.5875C>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_007067682.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970

Genes affected

LOC124904944 (HGNC:):

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 = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904944	XR_007067682.1	n.5875C>A		non_coding_transcript_exon_variant	2/2
LOC124904944	XR_007067681.1	n.5326C>A		non_coding_transcript_exon_variant	2/2
LOC124904944	XR_007067683.1	n.4827C>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR646HG	ENST00000659856.1	n.354-47930C>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.782

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.579

Gnomad4 OTH AF: 0.516

Alfa AF: 0.555 Hom.: 21302

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs348790; hg19: chr20-59054515;