Variant chr7-28186192-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NR_034097.1(JAZF1-AS1):n.166+440C>T 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 0.0322 in 152,210 control chromosomes in the GnomAD database, including 108 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 0.032 ( 108 hom., cov: 32)

Consequence

JAZF1-AS1
NR_034097.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -5.01

Variant links:

Genes affected

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

JAZF1-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.05).

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0322 (4896/152210) while in subpopulation NFE AF= 0.0495 (3365/68012). AF 95% confidence interval is 0.0481. There are 108 homozygotes in gnomad4. There are 2231 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 108 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
JAZF1-AS1	NR_034097.1 linkuse as main transcript	n.166+440C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
JAZF1-AS1	ENST00000444500.3 linkuse as main transcript	n.180+440C>T	intron_variant, non_coding_transcript_variant	1
JAZF1-AS1	ENST00000455963.6 linkuse as main transcript	n.301+440C>T	intron_variant, non_coding_transcript_variant	2
JAZF1-AS1	ENST00000436758.2 linkuse as main transcript	n.202+440C>T	intron_variant, non_coding_transcript_variant	2
JAZF1-AS1	ENST00000657365.1 linkuse as main transcript	n.36+440C>T	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0322

AC:

4902

AN:

152092

Hom.:

108

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00995

Gnomad AMI

AF:

0.0252

Gnomad AMR

AF:

0.0363

Gnomad ASJ

AF:

0.0429

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.0313

Gnomad FIN

AF:

0.0104

Gnomad MID

AF:

0.0764

Gnomad NFE

AF:

0.0495

Gnomad OTH

AF:

0.0536

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

GnomAD4 genome

AF:

0.0322

AC:

4896

AN:

152210

Hom.:

108

Cov.:

AF XY:

0.0300

AC XY:

2231

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.00992

Gnomad4 AMR

AF:

0.0363

Gnomad4 ASJ

AF:

0.0429

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0311

Gnomad4 FIN

AF:

0.0104

Gnomad4 NFE

AF:

0.0495

Gnomad4 OTH

AF:

0.0531

Alfa

AF:

0.0282

Hom.:

Bravo

AF:

0.0331

Asia WGS

AF:

0.0170

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.012

DANN

Benign

0.36

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over