rs10490125

Variant names:

• chr2-48897059-T-A
• rs10490125
• ENST00000634588.1:n.303-49157T>A

Your query was ambiguous. Multiple possible variants found:

• chr2-48897059-T-A
• chr2-48897059-T-G

Variant summary

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

The ENST00000634588.1(MIR548BAHG):​n.303-49157T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.027 in 152,318 control chromosomes in the GnomAD database, including 117 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 0.027 (117 hom., cov: 32)
• Consequence: MIR548BAHG ENST00000634588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700
• Publications: 0 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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.113 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.303-49157T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0269 AC: 4098 AN: 152200 Hom.: 114 Cov.: 32

Gnomad AFR AF: 0.00765

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.0185

Gnomad ASJ AF: 0.00606

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.0891

Gnomad FIN AF: 0.0222

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0290

Gnomad OTH AF: 0.0335

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

GnomAD4 genome AF: 0.0270 AC: 4105 AN: 152318 Hom.: 117 Cov.: 32 AF XY: 0.0284 AC XY: 2114 AN XY: 74488

African (AFR) AF: 0.00765 AC: 318 AN: 41576

American (AMR) AF: 0.0184 AC: 282 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00606 AC: 21 AN: 3468

East Asian (EAS) AF: 0.121 AC: 625 AN: 5172

South Asian (SAS) AF: 0.0883 AC: 426 AN: 4824

European-Finnish (FIN) AF: 0.0222 AC: 236 AN: 10624

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0290 AC: 1975 AN: 68038

Other (OTH) AF: 0.0378 AC: 80 AN: 2114

Alfa AF: 0.0232 Hom.: 9

Bravo AF: 0.0260

Asia WGS AF: 0.124 AC: 432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.9
DANN	Benign	0.85
PhyloP100		0.070

Splicing

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

Other links and lift over

dbSNP: rs10490125; hg19: chr2-49124198;