rs849334

Positions:

• chr7-28184223-T-C
• chr7-28184223-T-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.84-1447T>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 0.903 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 NR_034097.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.711

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=-0.53).
• 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/exons	MANE	UniProt
JAZF1-AS1	NR_034097.1	n.84-1447T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
JAZF1-AS1	ENST00000444500.3	n.98-1447T>C		intron_variant, non_coding_transcript_variant		1
JAZF1-AS1	ENST00000455963.6	n.219-1447T>C		intron_variant, non_coding_transcript_variant		2
JAZF1-AS1	ENST00000436758.2	n.120-1447T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.971

Gnomad4 AMR AF: 0.919

Gnomad4 ASJ AF: 0.890

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.870

Gnomad4 FIN AF: 0.860

Gnomad4 NFE AF: 0.861

Gnomad4 OTH AF: 0.888

Alfa AF: 0.890 Hom.: 10374

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs849334; hg19: chr7-28223842;