chr11-74399308-A-G

Position:

• chr11-74399308-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

MIR548AL (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR548AL	NR_039710.1	n.72A>G		non_coding_transcript_exon_variant	1/1
MIR548AL	unassigned_transcript_1933	n.8A>G		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR548AL	ENST00000578416.1	n.72A>G		non_coding_transcript_exon_variant	1/1	6
ENSG00000255440	ENST00000524441.2	n.105+379A>G		intron_variant		2
ENSG00000254631	ENST00000531906.5	n.258+1403A>G		intron_variant		4

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

GnomAD3 exomes AF: 0.159 AC: 58 AN: 364 Hom.: 3 AF XY: 0.167 AC XY: 34 AN XY: 204

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

Gnomad4 AFR exome AF: 0.122

Gnomad4 AMR exome AF: 0.375

Gnomad4 ASJ exome AF: 0.250

Gnomad4 SAS exome AF: 0.223

Gnomad4 NFE exome AF: 0.141

Gnomad4 OTH exome AF: 0.112

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

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.134

Alfa AF: 0.144 Hom.: 1593

Bravo AF: 0.145

Asia WGS AF: 0.258 AC: 897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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