7-28199241-A-G

Position:

• chr7-28199241-A-G

Variant summary

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

The NR_034097.1(JAZF1-AS1):​n.166+13489A>G 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 0.855 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 NR_034097.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
JAZF1-AS1	NR_034097.1	n.166+13489A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
JAZF1-AS1	ENST00000444500.3	n.180+13489A>G		intron_variant, non_coding_transcript_variant		1
JAZF1-AS1	ENST00000455963.6	n.301+13489A>G		intron_variant, non_coding_transcript_variant		2
JAZF1-AS1	ENST00000436758.2	n.202+13489A>G		intron_variant, non_coding_transcript_variant		2
JAZF1-AS1	ENST00000657365.1	n.36+13489A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.895

Gnomad4 ASJ AF: 0.886

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.867

Gnomad4 FIN AF: 0.849

Gnomad4 NFE AF: 0.844

Gnomad4 OTH AF: 0.850

Alfa AF: 0.853 Hom.: 75662

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs849315; hg19: chr7-28238860;