chr4-41756786-T-C

Position:

• chr4-41756786-T-C

Variant summary

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

The ENST00000508038.1(PHOX2B-AS1):​n.294+8200T>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 0.114 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 ENST00000508038.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260

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=-0.89).
• 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/exons	MANE	Protein	UniProt
PHOX2B-AS1	XR_001741671.2	n.238+8200T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PHOX2B-AS1	ENST00000508038.1	n.294+8200T>C		intron_variant, non_coding_transcript_variant		5
	ENST00000510602.1	n.171-165T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.0753

Gnomad4 ASJ AF: 0.0979

Gnomad4 EAS AF: 0.000773

Gnomad4 SAS AF: 0.0721

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.0970

Alfa AF: 0.0988 Hom.: 1107

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9283670; hg19: chr4-41758803;