rs2823756

Variant names:

• chr21-16370010-A-G
• rs2823756
• ENST00000400178.7:n.664-21604A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000400178.7(MIR99AHG):​n.664-21604A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 152,128 control chromosomes in the GnomAD database, including 10,930 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 0.35 (10930 hom., cov: 33)
• Consequence: MIR99AHG ENST00000400178.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.854
• Publications: 11 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR99AHG	NR_027790.3	n.470-117480A>G		intron_variant	Intron 4 of 7
MIR99AHG	NR_027791.3	n.316-21604A>G		intron_variant	Intron 2 of 5
MIR99AHG	NR_111004.2	n.443-21604A>G		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR99AHG	ENST00000400178.7	n.664-21604A>G		intron_variant	Intron 4 of 6	3
MIR99AHG	ENST00000413645.2	n.157-21604A>G		intron_variant	Intron 2 of 3	3
MIR99AHG	ENST00000419952.6	n.316-21604A>G		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53767 AN: 152010 Hom.: 10908 Cov.: 33

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.354 AC: 53828 AN: 152128 Hom.: 10930 Cov.: 33 AF XY: 0.352 AC XY: 26152 AN XY: 74364

African (AFR) AF: 0.557 AC: 23097 AN: 41482

American (AMR) AF: 0.323 AC: 4940 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 986 AN: 3466

East Asian (EAS) AF: 0.251 AC: 1300 AN: 5188

South Asian (SAS) AF: 0.168 AC: 812 AN: 4820

European-Finnish (FIN) AF: 0.321 AC: 3394 AN: 10580

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.268 AC: 18236 AN: 67978

Other (OTH) AF: 0.328 AC: 693 AN: 2116

Alfa AF: 0.284 Hom.: 10129

Bravo AF: 0.364

Asia WGS AF: 0.250 AC: 869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	18
DANN	Benign	0.89
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs2823756; hg19: chr21-17742330;