rs1381100

Variant names:

• chr20-60264818-C-T
• rs1381100
• ENST00000421257.1:n.36-48492C>T

Variant summary

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

The ENST00000421257.1(MIR646HG):​n.36-48492C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 152,102 control chromosomes in the GnomAD database, including 13,953 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 0.37 (13953 hom., cov: 33)
• Consequence: MIR646HG ENST00000421257.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950
• Publications: 6 publications found

Genes affected

MIR646HG (HGNC:27659): (MIR646 host gene)

LOC105372698 (HGNC:):

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 = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR646HG	NR_046099.1	n.333-54103C>T		intron_variant	Intron 3 of 4
LOC105372698	NR_171673.1	n.63+8965C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR646HG	ENST00000421257.1	n.36-48492C>T		intron_variant	Intron 1 of 2	3
MIR646HG	ENST00000432910.5	n.333-54103C>T		intron_variant	Intron 3 of 4	2
MIR646HG	ENST00000437035.5	n.37-48492C>T		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55711 AN: 151984 Hom.: 13898 Cov.: 33

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.367 AC: 55836 AN: 152102 Hom.: 13953 Cov.: 33 AF XY: 0.359 AC XY: 26721 AN XY: 74358

African (AFR) AF: 0.720 AC: 29860 AN: 41466

American (AMR) AF: 0.312 AC: 4768 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 746 AN: 3472

East Asian (EAS) AF: 0.225 AC: 1161 AN: 5162

South Asian (SAS) AF: 0.289 AC: 1393 AN: 4822

European-Finnish (FIN) AF: 0.230 AC: 2437 AN: 10588

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14582 AN: 67980

Other (OTH) AF: 0.328 AC: 692 AN: 2110

Alfa AF: 0.278 Hom.: 19020

Bravo AF: 0.390

Asia WGS AF: 0.300 AC: 1045 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	0.78
DANN	Benign	0.41
PhyloP100		-0.095

Splicing

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

Other links and lift over

dbSNP: rs1381100; hg19: chr20-58839876;