ENST00000400178.7:n.663+3798C>T

Variant names:

• chr21-16234913-C-T
• rs238973
• ENST00000400178.7:n.663+3798C>T

Variant summary

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

The ENST00000400178.7(MIR99AHG):​n.663+3798C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.748 in 151,790 control chromosomes in the GnomAD database, including 48,534 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 0.75 (48534 hom., cov: 31)
• Consequence: MIR99AHG ENST00000400178.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.594
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR99AHG	NR_027790.3	n.469+3798C>T		intron_variant	Intron 4 of 7
MIR99AHG	NR_027791.3	n.315+3798C>T		intron_variant	Intron 2 of 5
MIR99AHG	NR_111004.2	n.442+3798C>T		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR99AHG	ENST00000400178.7	n.663+3798C>T		intron_variant	Intron 4 of 6	3
MIR99AHG	ENST00000413645.2	n.156+3798C>T		intron_variant	Intron 2 of 3	3
MIR99AHG	ENST00000419952.6	n.315+3798C>T		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.749 AC: 113529 AN: 151672 Hom.: 48527 Cov.: 31

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.977

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.935

Gnomad FIN AF: 0.925

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.933

Gnomad OTH AF: 0.810

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

GnomAD4 genome AF: 0.748 AC: 113552 AN: 151790 Hom.: 48534 Cov.: 31 AF XY: 0.753 AC XY: 55833 AN XY: 74166

African (AFR) AF: 0.293 AC: 12122 AN: 41354

American (AMR) AF: 0.887 AC: 13495 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.871 AC: 3021 AN: 3470

East Asian (EAS) AF: 0.860 AC: 4433 AN: 5154

South Asian (SAS) AF: 0.935 AC: 4503 AN: 4816

European-Finnish (FIN) AF: 0.925 AC: 9763 AN: 10552

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.933 AC: 63355 AN: 67914

Other (OTH) AF: 0.813 AC: 1716 AN: 2110

Alfa AF: 0.847 Hom.: 22384

Bravo AF: 0.723

Asia WGS AF: 0.868 AC: 3015 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.58
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs238973; hg19: chr21-17607233;