16-50062219-C-G

Position:

• chr16-50062219-C-G

Variant summary

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

The ENST00000568130.2(HEATR3-AS1):​n.289+2472G>C variant causes a intron, non coding transcript 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 ENST00000568130.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HEATR3-AS1	ENST00000568130.2	n.289+2472G>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.0487

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.0979

Gnomad4 FIN AF: 0.0460

Gnomad4 NFE AF: 0.0792

Gnomad4 OTH AF: 0.126

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9925215; hg19: chr16-50096130;