chr21-16505474-C-T

Variant names:

• chr21-16505474-C-T
• rs2823850
• ENST00000400178.7:n.784+17936C>T

Variant summary

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

The ENST00000445461.7(MIR99AHG):​n.460+17936C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 151,970 control chromosomes in the GnomAD database, including 10,933 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 (10933 hom., cov: 32)
• Consequence: MIR99AHG ENST00000445461.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

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

ENSG00000287066 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR99AHG	NR_027790.3	n.518+17936C>T		intron_variant	Intron 5 of 7
MIR99AHG	NR_027791.3	n.436+17936C>T		intron_variant	Intron 4 of 5
MIR99AHG	NR_111004.2	n.563+17936C>T		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR99AHG	ENST00000400178.7	n.784+17936C>T		intron_variant	Intron 6 of 6	3
MIR99AHG	ENST00000413645.2	n.228+113789C>T		intron_variant	Intron 3 of 3	3
MIR99AHG	ENST00000418813.6	n.389+17936C>T		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32400 AN: 151852 Hom.: 10882 Cov.: 32

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0981

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.0613

Gnomad SAS AF: 0.0726

Gnomad FIN AF: 0.000661

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.00383

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.214 AC: 32502 AN: 151970 Hom.: 10933 Cov.: 32 AF XY: 0.210 AC XY: 15601 AN XY: 74292

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.0977

Gnomad4 ASJ AF: 0.0133

Gnomad4 EAS AF: 0.0611

Gnomad4 SAS AF: 0.0720

Gnomad4 FIN AF: 0.000661

Gnomad4 NFE AF: 0.00381

Gnomad4 OTH AF: 0.159

Alfa AF: 0.0304 Hom.: 2328

Bravo AF: 0.242

Asia WGS AF: 0.113 AC: 398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.059
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2823850; hg19: chr21-17877794;