7-28189423-G-A

Variant names:

• chr7-28189423-G-A
• rs550448
• ENST00000444500.3:n.180+3671G>A

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+3671G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.864 in 152,142 control chromosomes in the GnomAD database, including 56,940 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 0.86 (56940 hom., cov: 31)
• Consequence: JAZF1-AS1 ENST00000444500.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17
• Publications: 17 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=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000444500.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JAZF1-AS1	NR_034097.1		n.166+3671G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JAZF1-AS1	ENST00000444500.3	TSL:1	n.180+3671G>A		intron	N/A
	JAZF1-AS1	ENST00000436758.2	TSL:2	n.202+3671G>A		intron	N/A
	JAZF1-AS1	ENST00000455963.6	TSL:2	n.301+3671G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.864 AC: 131380 AN: 152024 Hom.: 56893 Cov.: 31

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.916

Gnomad AMR AF: 0.899

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.860

Gnomad OTH AF: 0.860

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

GnomAD4 genome AF: 0.864 AC: 131483 AN: 152142 Hom.: 56940 Cov.: 31 AF XY: 0.864 AC XY: 64239 AN XY: 74384

African (AFR) AF: 0.839 AC: 34790 AN: 41462

American (AMR) AF: 0.899 AC: 13760 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.888 AC: 3080 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5169 AN: 5176

South Asian (SAS) AF: 0.870 AC: 4190 AN: 4814

European-Finnish (FIN) AF: 0.860 AC: 9106 AN: 10588

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

European-Non Finnish (NFE) AF: 0.860 AC: 58510 AN: 68016

Other (OTH) AF: 0.858 AC: 1808 AN: 2108

Alfa AF: 0.865 Hom.: 105425

Bravo AF: 0.868

Asia WGS AF: 0.941 AC: 3273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	7.1
DANN	Benign	0.58
PhyloP100		1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs550448;

hg19: chr7-28229042;