chr20-60337602-A-G

Variant names:

• chr20-60337602-A-G
• rs354747
• XR_007067684.1:n.6516T>C

Variant summary

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

The XR_007067684.1(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_007067684.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 7 publications found

Genes affected

LOC105372697 (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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 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.427+16744A>G		intron	N/A
	MIR646HG	ENST00000654960.1		n.354-40473A>G		intron	N/A
	MIR646HG	ENST00000659856.1		n.353+156689A>G		intron	N/A

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

African (AFR) AF: 0.819 AC: 33951 AN: 41458

American (AMR) AF: 0.406 AC: 6198 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1806 AN: 3466

East Asian (EAS) AF: 0.111 AC: 572 AN: 5170

South Asian (SAS) AF: 0.298 AC: 1427 AN: 4796

European-Finnish (FIN) AF: 0.416 AC: 4372 AN: 10518

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24678 AN: 67960

Other (OTH) AF: 0.480 AC: 1009 AN: 2104

Alfa AF: 0.396 Hom.: 6908

Bravo AF: 0.507

Asia WGS AF: 0.286 AC: 999 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.9
DANN	Benign	0.48
PhyloP100		0.057

Splicing

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

Other links and lift over

dbSNP: rs354747; hg19: chr20-58912660;