rs171415

Variant names:

• chr20-60221481-A-C
• rs171415
• ENST00000421257.1:n.35+40568A>C

Your query was ambiguous. Multiple possible variants found:

• chr20-60221481-A-C
• chr20-60221481-A-G
• chr20-60221481-A-T

Variant summary

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

The ENST00000421257.1(MIR646HG):​n.35+40568A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.825 in 152,174 control chromosomes in the GnomAD database, including 52,145 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 0.83 (52145 hom., cov: 33)
• Consequence: MIR646HG ENST00000421257.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.706
• Publications: 5 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 (SAS) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR646HG	NR_046099.1	n.332+40568A>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR646HG	ENST00000421257.1	n.35+40568A>C		intron_variant	Intron 1 of 2	3
MIR646HG	ENST00000427820.1	n.27-25312A>C		intron_variant	Intron 1 of 3	5
MIR646HG	ENST00000431181.5	n.767-24557A>C		intron_variant	Intron 7 of 7	3

Frequencies

GnomAD3 genomes AF: 0.825 AC: 125514 AN: 152056 Hom.: 52108 Cov.: 33

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.825 AC: 125598 AN: 152174 Hom.: 52145 Cov.: 33 AF XY: 0.824 AC XY: 61317 AN XY: 74402

African (AFR) AF: 0.779 AC: 32314 AN: 41484

American (AMR) AF: 0.799 AC: 12228 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.821 AC: 2849 AN: 3470

East Asian (EAS) AF: 0.607 AC: 3141 AN: 5172

South Asian (SAS) AF: 0.896 AC: 4315 AN: 4818

European-Finnish (FIN) AF: 0.847 AC: 8970 AN: 10594

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.867 AC: 58965 AN: 68020

Other (OTH) AF: 0.812 AC: 1717 AN: 2114

Alfa AF: 0.847 Hom.: 70946

Bravo AF: 0.814

Asia WGS AF: 0.761 AC: 2648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.33
DANN	Benign	0.72
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs171415; hg19: chr20-58796539;