ENST00000444500.3:n.98-1447T>C

Variant names:

• chr7-28184223-T-C
• rs849334
• ENST00000444500.3:n.98-1447T>C

Variant summary

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

The ENST00000444500.3(JAZF1-AS1):​n.98-1447T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.903 in 152,278 control chromosomes in the GnomAD database, including 62,353 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 0.90 (62353 hom., cov: 32)
• Consequence: JAZF1-AS1 ENST00000444500.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.711
• Publications: 8 publications found

Genes affected

JAZF1-AS1 (HGNC:41218): (JAZF1 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
JAZF1-AS1	NR_034097.1	n.84-1447T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JAZF1-AS1	ENST00000444500.3	n.98-1447T>C		intron_variant	Intron 1 of 4	1
JAZF1-AS1	ENST00000436758.2	n.120-1447T>C		intron_variant	Intron 1 of 3	2
JAZF1-AS1	ENST00000455963.6	n.219-1447T>C		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.903 AC: 137410 AN: 152160 Hom.: 62297 Cov.: 32

Gnomad AFR AF: 0.971

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.919

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.891

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

GnomAD4 genome AF: 0.903 AC: 137524 AN: 152278 Hom.: 62353 Cov.: 32 AF XY: 0.902 AC XY: 67148 AN XY: 74458

African (AFR) AF: 0.971 AC: 40347 AN: 41552

American (AMR) AF: 0.919 AC: 14064 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.890 AC: 3089 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5175 AN: 5182

South Asian (SAS) AF: 0.870 AC: 4207 AN: 4834

European-Finnish (FIN) AF: 0.860 AC: 9121 AN: 10602

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.861 AC: 58568 AN: 68014

Other (OTH) AF: 0.888 AC: 1877 AN: 2114

Alfa AF: 0.894 Hom.: 12309

Bravo AF: 0.913

Asia WGS AF: 0.949 AC: 3302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	11
DANN	Benign	0.92
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs849334; hg19: chr7-28223842;