rs2825043

Variant names:

• chr21-18724605-G-A
• rs2825043
• ENST00000437492.6:n.151+13319C>T

Variant summary

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

The ENST00000437492.6(MIR548XHG):​n.151+13319C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 151,982 control chromosomes in the GnomAD database, including 8,376 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 0.33 (8376 hom., cov: 32)
• Consequence: MIR548XHG ENST00000437492.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493
• Publications: 2 publications found

Genes affected

MIR548XHG (HGNC:52006): (MIR548X host gene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR548XHG	NR_109925.1	n.141+13319C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR548XHG	ENST00000437492.6	n.151+13319C>T		intron_variant	Intron 2 of 4	1
MIR548XHG	ENST00000355189.7	n.502+13319C>T		intron_variant	Intron 3 of 4	3
MIR548XHG	ENST00000414582.1	n.383+13319C>T		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49874 AN: 151864 Hom.: 8368 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.328 AC: 49895 AN: 151982 Hom.: 8376 Cov.: 32 AF XY: 0.332 AC XY: 24643 AN XY: 74266

African (AFR) AF: 0.349 AC: 14464 AN: 41474

American (AMR) AF: 0.258 AC: 3929 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1139 AN: 3468

East Asian (EAS) AF: 0.405 AC: 2074 AN: 5120

South Asian (SAS) AF: 0.452 AC: 2170 AN: 4806

European-Finnish (FIN) AF: 0.361 AC: 3820 AN: 10568

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.310 AC: 21104 AN: 67974

Other (OTH) AF: 0.315 AC: 666 AN: 2114

Alfa AF: 0.324 Hom.: 3099

Bravo AF: 0.319

Asia WGS AF: 0.382 AC: 1328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.95
DANN	Benign	0.41
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs2825043; hg19: chr21-20096923;