rs354747

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372697	XR_007067684.1	n.6516T>C		non_coding_transcript_exon_variant	Exon 1 of 3
LOC105372697	XR_007067685.1	n.6516T>C		non_coding_transcript_exon_variant	Exon 1 of 3
LOC105372697	XR_007067686.1	n.6516T>C		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR646HG	ENST00000437035.5	n.427+16744A>G		intron_variant	Intron 4 of 4	5
MIR646HG	ENST00000654960.1	n.354-40473A>G		intron_variant	Intron 3 of 4
MIR646HG	ENST00000659856.1	n.353+156689A>G		intron_variant	Intron 3 of 5

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 v4.3

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;