rs7271202

chr20-60226585-G-A

Variant summary

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

The NR_046099.1(MIR646HG):n.332+45672G>A 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 0.333 in 151,916 control chromosomes in the GnomAD database, including 9,739 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 (9739 hom., cov: 33)
• Consequence: MIR646HG NR_046099.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR646HG	NR_046099.1	n.332+45672G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR646HG	ENST00000659856.1	n.353+45672G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50476 AN: 151798 Hom.: 9702 Cov.: 33

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.333 AC: 50585 AN: 151916 Hom.: 9739 Cov.: 33 AF XY: 0.334 AC XY: 24789 AN XY: 74232

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.303

Alfa AF: 0.262 Hom.: 2847

Bravo AF: 0.340

Asia WGS AF: 0.286 AC: 994 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	1.5
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7271202; hg19: chr20-58801643;