rs1381100

chr20-60264818-C-T

Variant summary

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

The NR_046099.1(MIR646HG):n.333-54103C>T 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 0.367 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 NR_046099.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950

Genes affected

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

LOC105372698 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
MIR646HG	NR_046099.1	n.333-54103C>T		intron_variant, non_coding_transcript_variant
LOC105372698	NR_171673.1	n.63+8965C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR646HG	ENST00000659856.1	n.353+83905C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.720

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.328

Alfa AF: 0.238 Hom.: 8145

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1381100; hg19: chr20-58839876;