16-50062219-C-G

Variant names:

• chr16-50062219-C-G
• rs9925215
• ENST00000568130.3:n.380+2472G>C

Variant summary

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

The ENST00000568130.3(HEATR3-AS1):​n.380+2472G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,188 control chromosomes in the GnomAD database, including 2,588 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 0.15 (2588 hom., cov: 33)
• Consequence: HEATR3-AS1 ENST00000568130.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442
• Publications: 5 publications found

Genes affected

HEATR3-AS1 (HGNC:55406): (HEATR3 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000568130.3. 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
	HEATR3-AS1	NR_186390.1		n.389+2472G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HEATR3-AS1	ENST00000568130.3	TSL:3	n.380+2472G>C		intron	N/A
	HEATR3-AS1	ENST00000719503.1		n.259+3834G>C		intron	N/A
	HEATR3-AS1	ENST00000719504.1		n.270+3834G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23157 AN: 152070 Hom.: 2589 Cov.: 33

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0487

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.0988

Gnomad FIN AF: 0.0460

Gnomad MID AF: 0.0764

Gnomad NFE AF: 0.0792

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.152 AC: 23195 AN: 152188 Hom.: 2588 Cov.: 33 AF XY: 0.150 AC XY: 11150 AN XY: 74402

African (AFR) AF: 0.318 AC: 13203 AN: 41492

American (AMR) AF: 0.118 AC: 1810 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0487 AC: 169 AN: 3470

East Asian (EAS) AF: 0.259 AC: 1341 AN: 5184

South Asian (SAS) AF: 0.0979 AC: 473 AN: 4832

European-Finnish (FIN) AF: 0.0460 AC: 487 AN: 10590

Middle Eastern (MID) AF: 0.0685 AC: 20 AN: 292

European-Non Finnish (NFE) AF: 0.0792 AC: 5387 AN: 68016

Other (OTH) AF: 0.126 AC: 267 AN: 2114

Alfa AF: 0.117 Hom.: 222

Bravo AF: 0.169

Asia WGS AF: 0.167 AC: 581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.31
PhyloP100		0.44

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9925215;

hg19: chr16-50096130;