ENST00000508038.2:n.294+8200T>C

Variant names:

• chr4-41756786-T-C
• rs9283670
• ENST00000508038.2:n.294+8200T>C

Variant summary

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

The ENST00000508038.2(PHOX2B-AS1):​n.294+8200T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,156 control chromosomes in the GnomAD database, including 1,101 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 0.11 (1101 hom., cov: 32)
• Consequence: PHOX2B-AS1 ENST00000508038.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 5 publications found

Genes affected

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

ENSG00000306586 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHOX2B-AS1	NR_187403.1	n.238+8200T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHOX2B-AS1	ENST00000508038.2	n.294+8200T>C		intron_variant	Intron 1 of 4	5
PHOX2B-AS1	ENST00000510602.1	n.171-165T>C		intron_variant	Intron 2 of 2	4
PHOX2B-AS1	ENST00000819353.1	n.241+8200T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17269 AN: 152038 Hom.: 1102 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.0754

Gnomad ASJ AF: 0.0979

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0720

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0980

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

GnomAD4 genome AF: 0.114 AC: 17284 AN: 152156 Hom.: 1101 Cov.: 32 AF XY: 0.112 AC XY: 8344 AN XY: 74376

African (AFR) AF: 0.161 AC: 6664 AN: 41500

American (AMR) AF: 0.0753 AC: 1151 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0979 AC: 340 AN: 3472

East Asian (EAS) AF: 0.000773 AC: 4 AN: 5172

South Asian (SAS) AF: 0.0721 AC: 347 AN: 4814

European-Finnish (FIN) AF: 0.125 AC: 1329 AN: 10590

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7120 AN: 67998

Other (OTH) AF: 0.0970 AC: 205 AN: 2114

Alfa AF: 0.102 Hom.: 1510

Bravo AF: 0.112

Asia WGS AF: 0.0370 AC: 128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.3
DANN	Benign	0.67
PhyloP100		-0.026

Splicing

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

Other links and lift over

dbSNP: rs9283670; hg19: chr4-41758803;