20-60225815-C-T

Variant names:

• chr20-60225815-C-T
• rs6100796
• ENST00000421257.1:n.35+44902C>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+44902C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 151,954 control chromosomes in the GnomAD database, including 9,686 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 0.33 (9686 hom., cov: 32)
• Consequence: MIR646HG ENST00000421257.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.340
• Publications: 3 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR646HG	NR_046099.1	n.332+44902C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR646HG	ENST00000421257.1	n.35+44902C>T		intron_variant	Intron 1 of 2	3
MIR646HG	ENST00000427820.1	n.27-20978C>T		intron_variant	Intron 1 of 3	5
MIR646HG	ENST00000431181.5	n.767-20223C>T		intron_variant	Intron 7 of 7	3

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50328 AN: 151836 Hom.: 9648 Cov.: 32

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.332 AC: 50439 AN: 151954 Hom.: 9686 Cov.: 32 AF XY: 0.333 AC XY: 24727 AN XY: 74272

African (AFR) AF: 0.538 AC: 22291 AN: 41406

American (AMR) AF: 0.303 AC: 4638 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 849 AN: 3472

East Asian (EAS) AF: 0.203 AC: 1045 AN: 5148

South Asian (SAS) AF: 0.253 AC: 1217 AN: 4814

European-Finnish (FIN) AF: 0.344 AC: 3628 AN: 10550

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15867 AN: 67954

Other (OTH) AF: 0.302 AC: 637 AN: 2110

Alfa AF: 0.290 Hom.: 1028

Bravo AF: 0.340

Asia WGS AF: 0.283 AC: 986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.7
DANN	Benign	0.84
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs6100796; hg19: chr20-58800873;