rs9283670

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr4-41756786-T-A
• chr4-41756786-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000508038.2(PHOX2B-AS1):​n.294+8200T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHOX2B-AS1	NR_187403.1	n.238+8200T>A		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>A		intron_variant	Intron 1 of 4	5
PHOX2B-AS1	ENST00000510602.1	n.171-165T>A		intron_variant	Intron 2 of 2	4
PHOX2B-AS1	ENST00000819353.1	n.241+8200T>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 1510

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.9
DANN	Benign	0.69
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;