ENST00000437035.5:n.427+50573C>A

Variant names:

• chr20-60371431-C-A
• rs55681231
• ENST00000437035.5:n.427+50573C>A

Variant summary

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

The ENST00000437035.5(MIR646HG):​n.427+50573C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,082 control chromosomes in the GnomAD database, including 7,649 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 0.31 (7649 hom., cov: 33)
• Consequence: MIR646HG ENST00000437035.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR646HG	ENST00000437035.5	n.427+50573C>A		intron_variant	Intron 4 of 4	5
MIR646HG	ENST00000654960.1	n.354-6644C>A		intron_variant	Intron 3 of 4
MIR646HG	ENST00000659856.1	n.354-155956C>A		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46487 AN: 151964 Hom.: 7651 Cov.: 33

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.306 AC: 46498 AN: 152082 Hom.: 7649 Cov.: 33 AF XY: 0.305 AC XY: 22668 AN XY: 74322

African (AFR) AF: 0.200 AC: 8318 AN: 41496

American (AMR) AF: 0.258 AC: 3951 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1636 AN: 3470

East Asian (EAS) AF: 0.118 AC: 612 AN: 5166

South Asian (SAS) AF: 0.251 AC: 1208 AN: 4822

European-Finnish (FIN) AF: 0.410 AC: 4329 AN: 10552

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25215 AN: 67984

Other (OTH) AF: 0.311 AC: 654 AN: 2104

Alfa AF: 0.335 Hom.: 15209

Bravo AF: 0.290

Asia WGS AF: 0.208 AC: 728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.57
DANN	Benign	0.31
PhyloP100		-0.016

Splicing

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

Other links and lift over

dbSNP: rs55681231; hg19: chr20-58946489;