rs1570160

chr20-60165348-A-C

Variant summary

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

The NR_046099.1(MIR646HG):n.253+10842A>C variant causes a intron, non coding transcript 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 NR_046099.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.357

Genes affected

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=-0.83).
• 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/exons	MANE	UniProt
MIR646HG	NR_046099.1	n.253+10842A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR646HG	ENST00000659856.1	n.274+10847A>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.364

Alfa AF: 0.421 Hom.: 2858

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1570160; hg19: chr20-58740406;