chr7-28199241-A-G

Variant names:

• chr7-28199241-A-G
• rs849315
• ENST00000444500.3:n.180+13489A>G

Variant summary

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

The ENST00000444500.3(JAZF1-AS1):​n.180+13489A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.855 in 151,768 control chromosomes in the GnomAD database, including 55,567 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 0.85 (55567 hom., cov: 28)
• Consequence: JAZF1-AS1 ENST00000444500.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580
• 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=-0.93).
• 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.166+13489A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JAZF1-AS1	ENST00000444500.3	n.180+13489A>G		intron_variant	Intron 2 of 4	1
JAZF1-AS1	ENST00000436758.2	n.202+13489A>G		intron_variant	Intron 2 of 3	2
JAZF1-AS1	ENST00000455963.6	n.301+13489A>G		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.855 AC: 129602 AN: 151650 Hom.: 55520 Cov.: 28

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.895

Gnomad ASJ AF: 0.886

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.868

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.853

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

GnomAD4 genome AF: 0.855 AC: 129706 AN: 151768 Hom.: 55567 Cov.: 28 AF XY: 0.854 AC XY: 63365 AN XY: 74158

African (AFR) AF: 0.836 AC: 34582 AN: 41348

American (AMR) AF: 0.895 AC: 13679 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.886 AC: 3072 AN: 3468

East Asian (EAS) AF: 0.999 AC: 5095 AN: 5102

South Asian (SAS) AF: 0.867 AC: 4160 AN: 4798

European-Finnish (FIN) AF: 0.849 AC: 8913 AN: 10502

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.844 AC: 57349 AN: 67964

Other (OTH) AF: 0.850 AC: 1786 AN: 2100

Alfa AF: 0.854 Hom.: 104965

Bravo AF: 0.860

Asia WGS AF: 0.941 AC: 3271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.37
PhyloP100		-0.058

Splicing

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

Other links and lift over

dbSNP: rs849315; hg19: chr7-28238860;