2-55987381-A-G

Variant names:

• chr2-55987381-A-G
• rs6545535
• ENST00000606639.1:n.82+35142A>G

Variant summary

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

The ENST00000606639.1(ENSG00000272180):​n.82+35142A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,056 control chromosomes in the GnomAD database, including 12,758 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 (12758 hom., cov: 33)
• Consequence: ENSG00000272180 ENST00000606639.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376
• Publications: 2 publications found

Genes affected

ENSG00000272180 (HGNC:):

MIR217HG (HGNC:50537): (MIR217 host gene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000606639.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR217HG	NR_126406.1		n.209-23499T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000272180	ENST00000606639.1	TSL:1	n.82+35142A>G		intron	N/A
	MIR217HG	ENST00000446139.2	TSL:5	n.925-23499T>C		intron	N/A
	MIR217HG	ENST00000701602.1		n.407+6492T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56076 AN: 151938 Hom.: 12732 Cov.: 33

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.0631

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.369 AC: 56162 AN: 152056 Hom.: 12758 Cov.: 33 AF XY: 0.362 AC XY: 26918 AN XY: 74336

African (AFR) AF: 0.640 AC: 26534 AN: 41470

American (AMR) AF: 0.278 AC: 4254 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1073 AN: 3468

East Asian (EAS) AF: 0.0628 AC: 324 AN: 5156

South Asian (SAS) AF: 0.395 AC: 1905 AN: 4822

European-Finnish (FIN) AF: 0.178 AC: 1883 AN: 10556

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19142 AN: 67996

Other (OTH) AF: 0.342 AC: 721 AN: 2108

Alfa AF: 0.312 Hom.: 24863

Bravo AF: 0.381

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.74
DANN	Benign	0.80
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs6545535; hg19: chr2-56214516;