rs2823897

Positions:

• chr21-16590062-T-A

Variant summary

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

The NR_136541.1(MIR99AHG):​n.644-16932T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0421 in 152,286 control chromosomes in the GnomAD database, including 308 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 0.042 (308 hom., cov: 32)
• Consequence: MIR99AHG NR_136541.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.09

Genes affected

MIR99AHG (HGNC:1274): (mir-99a-let-7c cluster host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR99AHG	NR_136541.1	n.644-16932T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR99AHG	ENST00000653129.1	n.931-16932T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0420 AC: 6397 AN: 152168 Hom.: 303 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0202

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.0148

Gnomad SAS AF: 0.0242

Gnomad FIN AF: 0.00264

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0131

Gnomad OTH AF: 0.0364

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

GnomAD4 genome AF: 0.0421 AC: 6417 AN: 152286 Hom.: 308 Cov.: 32 AF XY: 0.0411 AC XY: 3060 AN XY: 74470

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.0202

Gnomad4 ASJ AF: 0.0164

Gnomad4 EAS AF: 0.0148

Gnomad4 SAS AF: 0.0240

Gnomad4 FIN AF: 0.00264

Gnomad4 NFE AF: 0.0131

Gnomad4 OTH AF: 0.0360

Alfa AF: 0.0287 Hom.: 19

Bravo AF: 0.0469

Asia WGS AF: 0.0370 AC: 129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	16
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2823897; hg19: chr21-17962382;