rs2824985

Positions:

• chr21-18677588-G-A
• chr21-18677588-G-T
• chr21-18677588-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_109925.1(MIR548XHG):​n.141+60336C>T variant causes a intron, non coding transcript 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 NR_109925.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.985

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
MIR548XHG	NR_109925.1	n.141+60336C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR548XHG	ENST00000671206.1	n.644+60336C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.0719

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.421

Alfa AF: 0.372 Hom.: 1663

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2824985; hg19: chr21-20049906;