rs2823615

Variant names:

• chr21-16110813-A-T
• rs2823615
• ENST00000400178.7:n.506+39415A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000400178.7(MIR99AHG):​n.506+39415A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 151,950 control chromosomes in the GnomAD database, including 8,271 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 0.32 (8271 hom., cov: 32)
• Consequence: MIR99AHG ENST00000400178.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43
• Publications: 12 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR99AHG	NR_027790.3	n.312+39415A>T		intron_variant	Intron 2 of 7
MIR99AHG	NR_111004.2	n.285+39415A>T		intron_variant	Intron 1 of 5
MIR99AHG	NR_111005.2	n.285+39415A>T		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR99AHG	ENST00000400178.7	n.506+39415A>T		intron_variant	Intron 2 of 6	3
MIR99AHG	ENST00000456342.6	n.233+39415A>T		intron_variant	Intron 1 of 7	2
MIR99AHG	ENST00000602580.7	n.435+39415A>T		intron_variant	Intron 2 of 5	5

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48815 AN: 151832 Hom.: 8253 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.0736

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.322 AC: 48877 AN: 151950 Hom.: 8271 Cov.: 32 AF XY: 0.315 AC XY: 23371 AN XY: 74268

African (AFR) AF: 0.406 AC: 16846 AN: 41472

American (AMR) AF: 0.223 AC: 3406 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1068 AN: 3468

East Asian (EAS) AF: 0.0739 AC: 383 AN: 5180

South Asian (SAS) AF: 0.286 AC: 1377 AN: 4818

European-Finnish (FIN) AF: 0.226 AC: 2385 AN: 10542

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22440 AN: 67890

Other (OTH) AF: 0.274 AC: 578 AN: 2108

Alfa AF: 0.332 Hom.: 1140

Bravo AF: 0.325

Asia WGS AF: 0.186 AC: 640 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	13
DANN	Benign	0.78
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs2823615; hg19: chr21-17483133;