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. The variant received -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
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637474.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR493HG	ENST00000637474.1	TSL:5	n.108+17933G>A		intron	N/A

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

African (AFR) AF: 0.0406 AC: 1677 AN: 41274

American (AMR) AF: 0.272 AC: 4148 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 894 AN: 3462

East Asian (EAS) AF: 0.153 AC: 779 AN: 5098

South Asian (SAS) AF: 0.0665 AC: 316 AN: 4754

European-Finnish (FIN) AF: 0.122 AC: 1280 AN: 10508

Middle Eastern (MID) AF: 0.277 AC: 77 AN: 278

European-Non Finnish (NFE) AF: 0.212 AC: 14350 AN: 67772

Other (OTH) AF: 0.202 AC: 426 AN: 2104

Alfa AF: 0.166 Hom.: 861

Bravo AF: 0.168

Asia WGS AF: 0.128 AC: 448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.044
DANN	Benign	0.70
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs721909; hg19: chr14-101329803;