21-16350866-C-T

Variant names:

• chr21-16350866-C-T
• rs239410
• ENST00000400178.7:n.664-40748C>T

Variant summary

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

The ENST00000400178.7(MIR99AHG):​n.664-40748C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.813 in 152,038 control chromosomes in the GnomAD database, including 55,281 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 0.81 (55281 hom., cov: 32)
• Consequence: MIR99AHG ENST00000400178.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127
• Publications: 0 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.989 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000400178.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR99AHG	NR_027790.3		n.469+119751C>T		intron	N/A
	MIR99AHG	NR_027791.3		n.316-40748C>T		intron	N/A
	MIR99AHG	NR_111004.2		n.443-40748C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR99AHG	ENST00000400178.7	TSL:3	n.664-40748C>T		intron	N/A
	MIR99AHG	ENST00000413645.2	TSL:3	n.157-40748C>T		intron	N/A
	MIR99AHG	ENST00000419952.6	TSL:3	n.316-40748C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.813 AC: 123568 AN: 151920 Hom.: 55284 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.966

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.989

Gnomad FIN AF: 0.977

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.995

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.813 AC: 123588 AN: 152038 Hom.: 55281 Cov.: 32 AF XY: 0.814 AC XY: 60537 AN XY: 74340

African (AFR) AF: 0.401 AC: 16588 AN: 41362

American (AMR) AF: 0.850 AC: 12989 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.966 AC: 3353 AN: 3472

East Asian (EAS) AF: 0.946 AC: 4896 AN: 5174

South Asian (SAS) AF: 0.989 AC: 4774 AN: 4826

European-Finnish (FIN) AF: 0.977 AC: 10337 AN: 10580

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.995 AC: 67682 AN: 68024

Other (OTH) AF: 0.842 AC: 1781 AN: 2114

Alfa AF: 0.888 Hom.: 12257

Bravo AF: 0.783

Asia WGS AF: 0.893 AC: 3082 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.69
DANN	Benign	0.39
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs239410; hg19: chr21-17723187;