rs7271202

Variant names:

• chr20-60226585-G-A
• rs7271202
• ENST00000421257.1:n.35+45672G>A

Variant summary

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

The ENST00000432910.5(MIR646HG):​n.332+45672G>A variant causes a intron 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 ENST00000432910.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100
• 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=-0.92).
• 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 rank	MANE	Protein	UniProt
MIR646HG	NR_046099.1	n.332+45672G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR646HG	ENST00000421257.1	n.35+45672G>A		intron_variant	Intron 1 of 2	3
MIR646HG	ENST00000427820.1	n.27-20208G>A		intron_variant	Intron 1 of 3	5
MIR646HG	ENST00000431181.5	n.767-19453G>A		intron_variant	Intron 7 of 7	3

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

African (AFR) AF: 0.540 AC: 22373 AN: 41440

American (AMR) AF: 0.304 AC: 4642 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 848 AN: 3472

East Asian (EAS) AF: 0.211 AC: 1092 AN: 5174

South Asian (SAS) AF: 0.255 AC: 1228 AN: 4808

European-Finnish (FIN) AF: 0.344 AC: 3616 AN: 10508

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

European-Non Finnish (NFE) AF: 0.234 AC: 15879 AN: 67936

Other (OTH) AF: 0.303 AC: 640 AN: 2114

Alfa AF: 0.264 Hom.: 3254

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
PhyloP100		0.010

Splicing

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

Other links and lift over

dbSNP: rs7271202; hg19: chr20-58801643;