chr2-49270867-G-A

Variant names:

• chr2-49270867-G-A
• rs9636436
• ENST00000634588.1:n.493-137335G>A

Variant summary

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

The ENST00000634588.1(MIR548BAHG):​n.493-137335G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,100 control chromosomes in the GnomAD database, including 5,086 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 0.25 (5086 hom., cov: 33)
• Consequence: MIR548BAHG ENST00000634588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.888
• Publications: 4 publications found

Genes affected

MIR548BAHG (HGNC:58158):

ENSG00000282998 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.334 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.493-137335G>A		intron	N/A
	ENSG00000282998	ENST00000635306.2	TSL:5	n.408-52239C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38590 AN: 151982 Hom.: 5084 Cov.: 33

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.311

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.254 AC: 38615 AN: 152100 Hom.: 5086 Cov.: 33 AF XY: 0.255 AC XY: 18964 AN XY: 74342

African (AFR) AF: 0.301 AC: 12489 AN: 41516

American (AMR) AF: 0.170 AC: 2590 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 888 AN: 3472

East Asian (EAS) AF: 0.347 AC: 1792 AN: 5160

South Asian (SAS) AF: 0.234 AC: 1131 AN: 4824

European-Finnish (FIN) AF: 0.310 AC: 3268 AN: 10556

Middle Eastern (MID) AF: 0.310 AC: 90 AN: 290

European-Non Finnish (NFE) AF: 0.231 AC: 15729 AN: 67982

Other (OTH) AF: 0.255 AC: 539 AN: 2112

Alfa AF: 0.238 Hom.: 14055

Bravo AF: 0.248

Asia WGS AF: 0.281 AC: 977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.15
DANN	Benign	0.58
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs9636436; hg19: chr2-49498006;