rs550448

Positions:

• chr7-28189423-G-A
• chr7-28189423-G-C
• chr7-28189423-G-T

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+3671G>A 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 0.864 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 NR_034097.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17

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=-0.61).
• 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	Protein	UniProt
JAZF1-AS1	NR_034097.1	n.166+3671G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
JAZF1-AS1	ENST00000444500.3	n.180+3671G>A		intron_variant, non_coding_transcript_variant		1
JAZF1-AS1	ENST00000455963.6	n.301+3671G>A		intron_variant, non_coding_transcript_variant		2
JAZF1-AS1	ENST00000436758.2	n.202+3671G>A		intron_variant, non_coding_transcript_variant		2
JAZF1-AS1	ENST00000657365.1	n.36+3671G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.839

Gnomad4 AMR AF: 0.899

Gnomad4 ASJ AF: 0.888

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.870

Gnomad4 FIN AF: 0.860

Gnomad4 NFE AF: 0.860

Gnomad4 OTH AF: 0.858

Alfa AF: 0.866 Hom.: 50009

Bravo AF: 0.868

Asia WGS AF: 0.941 AC: 3273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs550448; hg19: chr7-28229042;