rs7281501

Variant names:

• chr21-16285831-T-G
• rs7281501
• ENST00000400178.7:n.663+54716T>G

Variant summary

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

The ENST00000445461.7(MIR99AHG):​n.339+91198T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0517 in 152,246 control chromosomes in the GnomAD database, including 336 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 0.052 (336 hom., cov: 32)
• Consequence: MIR99AHG ENST00000445461.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR99AHG	NR_027790.3	n.469+54716T>G		intron_variant	Intron 4 of 7
MIR99AHG	NR_027791.3	n.315+54716T>G		intron_variant	Intron 2 of 5
MIR99AHG	NR_111004.2	n.442+54716T>G		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR99AHG	ENST00000400178.7	n.663+54716T>G		intron_variant	Intron 4 of 6	3
MIR99AHG	ENST00000413645.2	n.156+54716T>G		intron_variant	Intron 2 of 3	3
MIR99AHG	ENST00000419952.6	n.315+54716T>G		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.0517 AC: 7871 AN: 152128 Hom.: 336 Cov.: 32

Gnomad AFR AF: 0.0129

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0573

Gnomad ASJ AF: 0.0617

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.0446

Gnomad FIN AF: 0.0188

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0653

Gnomad OTH AF: 0.0656

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

GnomAD4 genome AF: 0.0517 AC: 7866 AN: 152246 Hom.: 336 Cov.: 32 AF XY: 0.0518 AC XY: 3857 AN XY: 74446

Gnomad4 AFR AF: 0.0128

Gnomad4 AMR AF: 0.0572

Gnomad4 ASJ AF: 0.0617

Gnomad4 EAS AF: 0.217

Gnomad4 SAS AF: 0.0447

Gnomad4 FIN AF: 0.0188

Gnomad4 NFE AF: 0.0653

Gnomad4 OTH AF: 0.0649

Alfa AF: 0.0633 Hom.: 317

Bravo AF: 0.0557

Asia WGS AF: 0.0970 AC: 337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.7
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7281501; hg19: chr21-17658152;