rs17483987

Variant names:

• chr2-48863314-C-T
• rs17483987
• ENST00000634588.1:n.302+53673C>T

Variant summary

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

The ENST00000634588.1(MIR548BAHG):​n.302+53673C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,190 control chromosomes in the GnomAD database, including 1,203 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 0.11 (1203 hom., cov: 33)
• Consequence: MIR548BAHG ENST00000634588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.992
• Publications: 1 publications found

Genes affected

MIR548BAHG (HGNC:58158):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000634588.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR548BAHG	ENST00000634588.1	TSL:5	n.302+53673C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16944 AN: 152072 Hom.: 1204 Cov.: 33

Gnomad AFR AF: 0.0378

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0950

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.111 AC: 16933 AN: 152190 Hom.: 1203 Cov.: 33 AF XY: 0.115 AC XY: 8540 AN XY: 74418

African (AFR) AF: 0.0378 AC: 1569 AN: 41554

American (AMR) AF: 0.0949 AC: 1450 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 604 AN: 3470

East Asian (EAS) AF: 0.173 AC: 893 AN: 5170

South Asian (SAS) AF: 0.149 AC: 717 AN: 4824

European-Finnish (FIN) AF: 0.197 AC: 2085 AN: 10584

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9269 AN: 67996

Other (OTH) AF: 0.115 AC: 242 AN: 2112

Alfa AF: 0.114 Hom.: 152

Bravo AF: 0.102

Asia WGS AF: 0.127 AC: 441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.90
DANN	Benign	0.47
PhyloP100		-0.99

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17483987;

hg19: chr2-49090453;