rs721909

Variant names:

• chr14-100863466-G-A
• rs721909
• ENST00000637474.1:n.108+17933G>A

Your query was ambiguous. Multiple possible variants found:

• chr14-100863466-G-A
• chr14-100863466-G-T

Variant summary

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

The ENST00000637474.1(MIR493HG):​n.108+17933G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 151,402 control chromosomes in the GnomAD database, including 2,475 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 0.16 (2475 hom., cov: 33)
• Consequence: MIR493HG ENST00000637474.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

Genes affected

MIR493HG (HGNC:55978): (MIR493 cluster host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR493HG	ENST00000637474.1	n.108+17933G>A		intron_variant	Intron 2 of 18	5

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24093 AN: 151278 Hom.: 2473 Cov.: 33

Gnomad AFR AF: 0.0407

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.0658

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.159 AC: 24110 AN: 151402 Hom.: 2475 Cov.: 33 AF XY: 0.155 AC XY: 11480 AN XY: 73968

Gnomad4 AFR AF: 0.0406

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.0665

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.202

Alfa AF: 0.139 Hom.: 398

Bravo AF: 0.168

Asia WGS AF: 0.128 AC: 448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.044
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs721909; hg19: chr14-101329803;