rs28462174

chr4-41749194-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000508038.1(PHOX2B-AS1):n.294+608G>A 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 0.0937 in 151,838 control chromosomes in the GnomAD database, including 729 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.094 (729 hom., cov: 32)
• Consequence: PHOX2B-AS1 ENST00000508038.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.275

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BP6: Variant 4-41749194-G-A is Benign according to our data. Variant chr4-41749194-G-A is described in ClinVar as [Benign]. Clinvar id is 1265356.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHOX2B-AS1	XR_001741671.2	n.238+608G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PHOX2B-AS1	ENST00000508038.1	n.294+608G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0938 AC: 14230 AN: 151718 Hom.: 731 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.0633

Gnomad ASJ AF: 0.0695

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0560

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0801

Gnomad NFE AF: 0.0905

Gnomad OTH AF: 0.0739

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

GnomAD4 genome AF: 0.0937 AC: 14233 AN: 151838 Hom.: 729 Cov.: 32 AF XY: 0.0926 AC XY: 6868 AN XY: 74206

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.0632

Gnomad4 ASJ AF: 0.0695

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0558

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.0906

Gnomad4 OTH AF: 0.0731

Alfa AF: 0.0940 Hom.: 93

Bravo AF: 0.0917

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Feb 02, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	7.1
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28462174; hg19: chr4-41751211;