rs55681231

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.88).
• 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

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.311

Alfa AF: 0.337 Hom.: 1930

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs55681231; hg19: chr20-58946489;