chr14-100863372-C-A

Variant names:

• chr14-100863372-C-A
• rs721910
• ENST00000637474.1:n.108+17839C>A

Variant summary

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

The ENST00000637474.1(MIR493HG):​n.108+17839C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,966 control chromosomes in the GnomAD database, including 17,261 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 0.46 (17261 hom., cov: 32)
• Consequence: MIR493HG ENST00000637474.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• Publications: 7 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.655 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+17839C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.455 AC: 69147 AN: 151848 Hom.: 17228 Cov.: 32

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.456 AC: 69247 AN: 151966 Hom.: 17261 Cov.: 32 AF XY: 0.448 AC XY: 33287 AN XY: 74248

African (AFR) AF: 0.661 AC: 27422 AN: 41464

American (AMR) AF: 0.468 AC: 7148 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1588 AN: 3466

East Asian (EAS) AF: 0.372 AC: 1920 AN: 5168

South Asian (SAS) AF: 0.230 AC: 1105 AN: 4812

European-Finnish (FIN) AF: 0.341 AC: 3591 AN: 10546

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25076 AN: 67932

Other (OTH) AF: 0.462 AC: 973 AN: 2106

Alfa AF: 0.398 Hom.: 15582

Bravo AF: 0.482

Asia WGS AF: 0.339 AC: 1177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.082
DANN	Benign	0.39
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs721910; hg19: chr14-101329709;