rs515924

Variant names:

• chr11-74399308-A-G
• rs515924
• ENST00000578416.1:n.72A>G

Variant summary

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

The NR_039710.1(MIR548AL):​n.72A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 154,346 control chromosomes in the GnomAD database, including 2,204 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 0.16 (2190 hom., cov: 32)
  • Exomes 𝑓: 0.11 (14 hom.)
• Consequence: MIR548AL NR_039710.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 14 publications found

Genes affected

MIR548AL (HGNC:41736): (microRNA 548al) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

ENSG00000255440 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_039710.1. 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
	MIR548AL	NR_039710.1		n.72A>G		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR548AL	ENST00000578416.1	TSL:6	n.72A>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000255440	ENST00000524441.2	TSL:2	n.105+379A>G		intron	N/A
	ENSG00000254631	ENST00000531906.5	TSL:4	n.258+1403A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24456 AN: 152058 Hom.: 2193 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.135

GnomAD2 exomes AF: 0.159 AC: 58 AN: 364 AF XY: 0.167

Gnomad AFR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.165

Gnomad OTH exome AF: 0.100

GnomAD4 exome AF: 0.108 AC: 234 AN: 2170 Hom.: 14 Cov.: 0 AF XY: 0.105 AC XY: 113 AN XY: 1076

African (AFR) AF: 0.122 AC: 9 AN: 74

American (AMR) AF: 0.375 AC: 3 AN: 8

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 1 AN: 4

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.223 AC: 21 AN: 94

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.0950 AC: 155 AN: 1632

European-Non Finnish (NFE) AF: 0.141 AC: 24 AN: 170

Other (OTH) AF: 0.112 AC: 21 AN: 188

GnomAD4 genome AF: 0.161 AC: 24458 AN: 152176 Hom.: 2190 Cov.: 32 AF XY: 0.169 AC XY: 12584 AN XY: 74400

African (AFR) AF: 0.117 AC: 4867 AN: 41530

American (AMR) AF: 0.139 AC: 2133 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 520 AN: 3466

East Asian (EAS) AF: 0.299 AC: 1548 AN: 5172

South Asian (SAS) AF: 0.255 AC: 1229 AN: 4824

European-Finnish (FIN) AF: 0.291 AC: 3080 AN: 10572

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10672 AN: 68006

Other (OTH) AF: 0.134 AC: 282 AN: 2110

Alfa AF: 0.143 Hom.: 2031

Bravo AF: 0.145

Asia WGS AF: 0.258 AC: 897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	13
DANN	Benign	0.95
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs515924; hg19: chr11-74110353; COSMIC: COSV53347052;