rs28599926

Positions:

• chr15-22225320-C-T

Variant summary

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

The NR_031672.1(MIR1268A):​n.10G>A 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 0.137 in 143,430 control chromosomes in the GnomAD database, including 247 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 0.14 (247 hom., cov: 40)
  • Exomes 𝑓: 0.034 (0 hom.)
• Consequence: MIR1268A NR_031672.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.742

Genes affected

MIR1268A (HGNC:):

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 = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR1268A	NR_031672.1	n.10G>A		non_coding_transcript_exon_variant	1/1
MIR1268A	unassigned_transcript_2658	n.6G>A		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR1268A	ENST00000408714.1	n.10G>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.138 AC: 19582 AN: 142048 Hom.: 244 Cov.: 40

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.0644

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0924

Gnomad MID AF: 0.0671

Gnomad NFE AF: 0.0589

Gnomad OTH AF: 0.123

GnomAD3 exomes AF: 0.0484 AC: 3 AN: 62 Hom.: 0 AF XY: 0.0909 AC XY: 2 AN XY: 22

Gnomad AFR exome AF: 0.250

Gnomad AMR exome AF: 0.00

Gnomad FIN exome AF: 0.100

Gnomad NFE exome AF: 0.0238

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0343 AC: 44 AN: 1282 Hom.: 0 Cov.: 0 AF XY: 0.0322 AC XY: 29 AN XY: 902

Gnomad4 AFR exome AF: 0.222

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.0625

Gnomad4 EAS exome AF: 0.0588

Gnomad4 SAS exome AF: 0.0313

Gnomad4 FIN exome AF: 0.0500

Gnomad4 NFE exome AF: 0.0267

Gnomad4 OTH exome AF: 0.0625

GnomAD4 genome AF: 0.138 AC: 19627 AN: 142148 Hom.: 247 Cov.: 40 AF XY: 0.139 AC XY: 9638 AN XY: 69396

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.0644

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.0924

Gnomad4 NFE AF: 0.0589

Gnomad4 OTH AF: 0.124

Alfa AF: 0.118 Hom.: 21

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	10
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28599926; hg19: chr15-22513271;