rs9680185

Variant names:

• chr21-18685360-A-T
• rs9680185
• ENST00000437492.6:n.151+52564T>A

Variant summary

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

The ENST00000437492.6(MIR548XHG):​n.151+52564T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0772 in 152,200 control chromosomes in the GnomAD database, including 1,096 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 0.077 (1096 hom., cov: 33)
• Consequence: MIR548XHG ENST00000437492.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.552

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR548XHG	NR_109925.1	n.141+52564T>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR548XHG	ENST00000437492.6	n.151+52564T>A		intron_variant	Intron 2 of 4	1
MIR548XHG	ENST00000355189.7	n.502+52564T>A		intron_variant	Intron 3 of 4	3
MIR548XHG	ENST00000414582.1	n.383+52564T>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.0770 AC: 11714 AN: 152084 Hom.: 1093 Cov.: 33

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0340

Gnomad ASJ AF: 0.00980

Gnomad EAS AF: 0.0633

Gnomad SAS AF: 0.0247

Gnomad FIN AF: 0.0433

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0140

Gnomad OTH AF: 0.0602

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

GnomAD4 genome AF: 0.0772 AC: 11748 AN: 152200 Hom.: 1096 Cov.: 33 AF XY: 0.0768 AC XY: 5717 AN XY: 74420

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.0341

Gnomad4 ASJ AF: 0.00980

Gnomad4 EAS AF: 0.0637

Gnomad4 SAS AF: 0.0241

Gnomad4 FIN AF: 0.0433

Gnomad4 NFE AF: 0.0140

Gnomad4 OTH AF: 0.0624

Alfa AF: 0.0488 Hom.: 79

Bravo AF: 0.0838

Asia WGS AF: 0.0770 AC: 267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.76
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9680185; hg19: chr21-20057678;