rs1001519

Variant names:

• chr20-60215413-C-T
• rs1001519
• ENST00000421257.1:n.35+34500C>T

Variant summary

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

The ENST00000432910.5(MIR646HG):​n.332+34500C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 152,032 control chromosomes in the GnomAD database, including 20,050 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 0.50 (20050 hom., cov: 32)
• Consequence: MIR646HG ENST00000432910.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 2 publications found

Genes affected

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 = 0.573 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000432910.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR646HG	NR_046099.1		n.332+34500C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR646HG	ENST00000421257.1	TSL:3	n.35+34500C>T		intron	N/A
	MIR646HG	ENST00000427820.1	TSL:5	n.27-31380C>T		intron	N/A
	MIR646HG	ENST00000431181.5	TSL:3	n.767-30625C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76062 AN: 151914 Hom.: 20024 Cov.: 32

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.0129

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.501 AC: 76147 AN: 152032 Hom.: 20050 Cov.: 32 AF XY: 0.489 AC XY: 36379 AN XY: 74320

African (AFR) AF: 0.579 AC: 24007 AN: 41458

American (AMR) AF: 0.387 AC: 5916 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1718 AN: 3470

East Asian (EAS) AF: 0.0131 AC: 68 AN: 5176

South Asian (SAS) AF: 0.401 AC: 1932 AN: 4812

European-Finnish (FIN) AF: 0.446 AC: 4711 AN: 10570

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.533 AC: 36201 AN: 67956

Other (OTH) AF: 0.464 AC: 979 AN: 2110

Alfa AF: 0.525 Hom.: 3496

Bravo AF: 0.494

Asia WGS AF: 0.252 AC: 882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.60
DANN	Benign	0.41
PhyloP100		-1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1001519;

hg19: chr20-58790471;