chr21-16620720-T-C

Variant names:

• chr21-16620720-T-C
• rs2211981
• ENST00000667313.1:n.1768T>C

Variant summary

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

The ENST00000667313.1(MIR99AHG):​n.1768T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.843 in 152,156 control chromosomes in the GnomAD database, including 57,570 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 0.84 (57570 hom., cov: 32)
• Consequence: MIR99AHG ENST00000667313.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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 = 0.979 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR99AHG	NR_136541.1	n.738-6996T>C		intron_variant	Intron 7 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR99AHG	ENST00000667313.1	n.1768T>C		non_coding_transcript_exon_variant	Exon 5 of 5
MIR99AHG	ENST00000670538.1	n.1675T>C		non_coding_transcript_exon_variant	Exon 7 of 7
MIR99AHG	ENST00000413645.2	n.229-19510T>C		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.843 AC: 128207 AN: 152038 Hom.: 57554 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.983

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.967

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.985

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.843 AC: 128253 AN: 152156 Hom.: 57570 Cov.: 32 AF XY: 0.847 AC XY: 62990 AN XY: 74402

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.916

Gnomad4 ASJ AF: 0.983

Gnomad4 EAS AF: 0.933

Gnomad4 SAS AF: 0.967

Gnomad4 FIN AF: 0.997

Gnomad4 NFE AF: 0.985

Gnomad4 OTH AF: 0.875

Alfa AF: 0.901 Hom.: 10233

Bravo AF: 0.820

Asia WGS AF: 0.915 AC: 3180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2211981; hg19: chr21-17993039;