2-49283034-A-G

Variant names:

• chr2-49283034-A-G
• rs7578654
• ENST00000634588.1:n.493-125168A>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000634588.1(MIR548BAHG):​n.493-125168A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MIR548BAHG ENST00000634588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.394
• Publications: 7 publications found

Genes affected

MIR548BAHG (HGNC:58158):

ENSG00000282998 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).

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.493-125168A>G		intron	N/A
	ENSG00000282998	ENST00000635306.2	TSL:5	n.407+48840T>C		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 344634 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 199046

African (AFR) AF: 0.00 AC: 0 AN: 9632

American (AMR) AF: 0.00 AC: 0 AN: 34814

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11076

East Asian (EAS) AF: 0.00 AC: 0 AN: 12420

South Asian (SAS) AF: 0.00 AC: 0 AN: 62700

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 15942

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2748

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 179772

Other (OTH) AF: 0.00 AC: 0 AN: 15530

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 49002

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	9.6
DANN	Benign	0.74
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs7578654; hg19: chr2-49510173;