rs16853571

Variant names:

• chr4-41751113-A-C
• rs16853571
• ENST00000819516.1:n.278T>G

Your query was ambiguous. Multiple possible variants found:

• chr4-41751113-A-C
• chr4-41751113-A-T

Variant summary

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

The ENST00000819516.1(ENSG00000306586):​n.278T>G variant causes a non coding transcript exon 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: ENSG00000306586 ENST00000819516.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 9 publications found

Genes affected

ENSG00000306586 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PHOX2B-AS1	NR_187403.1	n.238+2527A>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306586	ENST00000819516.1	n.278T>G		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000306586	ENST00000819517.1	n.33T>G		non_coding_transcript_exon_variant	Exon 2 of 2
PHOX2B-AS1	ENST00000508038.2	n.294+2527A>C		intron_variant	Intron 1 of 4	5

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

African (AFR) AF: 0.186 AC: 7742 AN: 41522

American (AMR) AF: 0.0610 AC: 933 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0818 AC: 284 AN: 3472

East Asian (EAS) AF: 0.00291 AC: 15 AN: 5158

South Asian (SAS) AF: 0.129 AC: 619 AN: 4816

European-Finnish (FIN) AF: 0.0541 AC: 574 AN: 10608

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0643 AC: 4373 AN: 68006

Other (OTH) AF: 0.0872 AC: 184 AN: 2110

Alfa AF: 0.0674 Hom.: 1235

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
PhyloP100		0.14
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs16853571; hg19: chr4-41753130;