rs354747

chr20-60337602-A-G

Variant summary

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

The XR_007067686.1(LOC105372697):n.6516T>C 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 0.491 in 151,944 control chromosomes in the GnomAD database, including 21,703 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 0.49 (21703 hom., cov: 32)
• Consequence: LOC105372697 XR_007067686.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570

Genes affected

LOC105372697 (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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372697	XR_007067686.1	n.6516T>C		non_coding_transcript_exon_variant	1/3
LOC105372697	XR_007067684.1	n.6516T>C		non_coding_transcript_exon_variant	1/3
LOC105372697	XR_007067685.1	n.6516T>C		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR646HG	ENST00000659856.1	n.353+156689A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74438 AN: 151826 Hom.: 21645 Cov.: 32

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.491 AC: 74561 AN: 151944 Hom.: 21703 Cov.: 32 AF XY: 0.486 AC XY: 36089 AN XY: 74228

Gnomad4 AFR AF: 0.819

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.521

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.480

Alfa AF: 0.392 Hom.: 6049

Bravo AF: 0.507

Asia WGS AF: 0.286 AC: 999 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	3.9
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs354747; hg19: chr20-58912660;