rs2823819

Positions:

• chr21-16455971-A-G

Variant summary

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

The NR_136541.1(MIR99AHG):​n.595-31519A>G 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 0.214 in 151,636 control chromosomes in the GnomAD database, including 3,955 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 0.21 (3955 hom., cov: 30)
• Consequence: MIR99AHG NR_136541.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

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=-0.49).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR99AHG	NR_136541.1	n.595-31519A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR99AHG	ENST00000653129.1	n.821-31519A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32482 AN: 151516 Hom.: 3943 Cov.: 30

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.214 AC: 32514 AN: 151636 Hom.: 3955 Cov.: 30 AF XY: 0.216 AC XY: 15970 AN XY: 74080

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.207

Alfa AF: 0.183 Hom.: 3360

Bravo AF: 0.214

Asia WGS AF: 0.209 AC: 731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	11
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2823819; hg19: chr21-17828291;