rs10583889

Positions:

• chr19-53725519-CTT-C
• chr19-53725519-CTT-CTTT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NR_030207.1(MIR516B2):​n.80_81delTT 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 0.00955 in 519,700 control chromosomes in the GnomAD database, including 218 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.025 (169 hom., cov: 32)
  • Exomes 𝑓: 0.0033 (49 hom.)
• Consequence: MIR516B2 NR_030207.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286

Genes affected

MIR516B2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR516B2	NR_030207.1	n.80_81delTT		non_coding_transcript_exon_variant	1/1
MIR516B2	unassigned_transcript_3368	n.*42_*43delTT		downstream_gene_variant
MIR516B2	unassigned_transcript_3369	n.*6_*7delTT		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR516B2	ENST00000385190.1	n.80_81delTT		non_coding_transcript_exon_variant	1/1	6
ENSG00000269842	ENST00000710708.1	n.585+12420_585+12421delTT		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0246 AC: 3736 AN: 152106 Hom.: 167 Cov.: 32

Gnomad AFR AF: 0.0859

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00642

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00166

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000456

Gnomad OTH AF: 0.0196

GnomAD3 exomes AF: 0.00391 AC: 948 AN: 242356 Hom.: 36 AF XY: 0.00260 AC XY: 341 AN XY: 131228

Gnomad AFR exome AF: 0.0576

Gnomad AMR exome AF: 0.00175

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000111

Gnomad SAS exome AF: 0.000485

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000135

Gnomad OTH exome AF: 0.00152

GnomAD4 exome AF: 0.00328 AC: 1206 AN: 367476 Hom.: 49 AF XY: 0.00243 AC XY: 504 AN XY: 207750

Gnomad4 AFR exome AF: 0.0851

Gnomad4 AMR exome AF: 0.00345

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000786

Gnomad4 SAS exome AF: 0.000963

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000192

Gnomad4 OTH exome AF: 0.00528

GnomAD4 genome AF: 0.0247 AC: 3756 AN: 152224 Hom.: 169 Cov.: 32 AF XY: 0.0236 AC XY: 1758 AN XY: 74426

Gnomad4 AFR AF: 0.0861

Gnomad4 AMR AF: 0.00635

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00145

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000456

Gnomad4 OTH AF: 0.0194

Alfa AF: 0.0132 Hom.: 14

Bravo AF: 0.0279

Asia WGS AF: 0.00924 AC: 32 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10583889; hg19: chr19-54228773;