rs2824985

Variant names:

• chr21-18677588-G-A
• rs2824985
• ENST00000437492.6:n.151+60336C>T

Your query was ambiguous. Multiple possible variants found:

• chr21-18677588-G-A
• chr21-18677588-G-C
• chr21-18677588-G-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+60336C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 151,454 control chromosomes in the GnomAD database, including 19,873 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 0.44 (19873 hom., cov: 31)
• Consequence: MIR548XHG ENST00000437492.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.985
• Publications: 0 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR548XHG	NR_109925.1	n.141+60336C>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+60336C>T		intron_variant	Intron 2 of 4	1
MIR548XHG	ENST00000355189.7	n.502+60336C>T		intron_variant	Intron 3 of 4	3
MIR548XHG	ENST00000414582.1	n.383+60336C>T		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67172 AN: 151336 Hom.: 19824 Cov.: 31

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.0718

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.444 AC: 67279 AN: 151454 Hom.: 19873 Cov.: 31 AF XY: 0.437 AC XY: 32342 AN XY: 74042

African (AFR) AF: 0.836 AC: 34659 AN: 41440

American (AMR) AF: 0.297 AC: 4507 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1659 AN: 3460

East Asian (EAS) AF: 0.0719 AC: 372 AN: 5172

South Asian (SAS) AF: 0.285 AC: 1370 AN: 4806

European-Finnish (FIN) AF: 0.295 AC: 3107 AN: 10538

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.300 AC: 20283 AN: 67540

Other (OTH) AF: 0.421 AC: 886 AN: 2104

Alfa AF: 0.390 Hom.: 1923

Bravo AF: 0.459

Asia WGS AF: 0.236 AC: 821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.22
PhyloP100		0.98

Splicing

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

Other links and lift over

dbSNP: rs2824985; hg19: chr21-20049906;