rs16853571

chr4-41751113-A-Cchr4-41751113-A-T

Variant summary

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

The ENST00000508038.1(PHOX2B-AS1):n.294+2527A>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 0.0972 in 152,196 control chromosomes in the GnomAD database, including 987 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 0.097 (987 hom., cov: 32)
• Consequence: PHOX2B-AS1 ENST00000508038.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145

Genes affected

PHOX2B-AS1 (HGNC:40457): (PHOX2B antisense RNA 1)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHOX2B-AS1	XR_001741671.2	n.238+2527A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PHOX2B-AS1	ENST00000508038.1	n.294+2527A>C		intron_variant, non_coding_transcript_variant		5
	ENST00000510602.1	n.53+716A>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0972 AC: 14783 AN: 152078 Hom.: 985 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0611

Gnomad ASJ AF: 0.0818

Gnomad EAS AF: 0.00271

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0541

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0643

Gnomad OTH AF: 0.0881

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

GnomAD4 genome AF: 0.0972 AC: 14794 AN: 152196 Hom.: 987 Cov.: 32 AF XY: 0.0949 AC XY: 7066 AN XY: 74438

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.0610

Gnomad4 ASJ AF: 0.0818

Gnomad4 EAS AF: 0.00291

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.0541

Gnomad4 NFE AF: 0.0643

Gnomad4 OTH AF: 0.0872

Alfa AF: 0.0636 Hom.: 742

Bravo AF: 0.0995

Asia WGS AF: 0.0870 AC: 302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	5.9
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16853571; hg19: chr4-41753130;