rs1570160

Variant names:

• chr20-60165348-A-C
• rs1570160
• ENST00000427691.5:n.455+10847A>C

Variant summary

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

The ENST00000427691.5(MIR646HG):​n.455+10847A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 151,912 control chromosomes in the GnomAD database, including 11,468 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 0.38 (11468 hom., cov: 32)
• Consequence: MIR646HG ENST00000427691.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.357
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR646HG	NR_046099.1	n.253+10842A>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR646HG	ENST00000427691.5	n.455+10847A>C		intron_variant	Intron 5 of 5	3
MIR646HG	ENST00000431181.5	n.766+41488A>C		intron_variant	Intron 7 of 7	3
MIR646HG	ENST00000432910.5	n.253+10842A>C		intron_variant	Intron 2 of 4	2

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56981 AN: 151792 Hom.: 11465 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.375 AC: 57018 AN: 151912 Hom.: 11468 Cov.: 32 AF XY: 0.370 AC XY: 27487 AN XY: 74244

African (AFR) AF: 0.254 AC: 10543 AN: 41450

American (AMR) AF: 0.333 AC: 5082 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1328 AN: 3466

East Asian (EAS) AF: 0.137 AC: 711 AN: 5172

South Asian (SAS) AF: 0.336 AC: 1620 AN: 4826

European-Finnish (FIN) AF: 0.453 AC: 4752 AN: 10500

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31618 AN: 67942

Other (OTH) AF: 0.364 AC: 764 AN: 2100

Alfa AF: 0.417 Hom.: 2887

Bravo AF: 0.361

Asia WGS AF: 0.259 AC: 903 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.54
PhyloP100		0.36
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1570160; hg19: chr20-58740406;