7-28186192-C-T

Position:

• chr7-28186192-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.01

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=-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	n.166+440C>T		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+440C>T		intron_variant, non_coding_transcript_variant		1
JAZF1-AS1	ENST00000455963.6	n.301+440C>T		intron_variant, non_coding_transcript_variant		2
JAZF1-AS1	ENST00000436758.2	n.202+440C>T		intron_variant, non_coding_transcript_variant		2
JAZF1-AS1	ENST00000657365.1	n.36+440C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0322 AC: 4902 AN: 152092 Hom.: 108 Cov.: 32

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.: 32 AF XY: 0.0300 AC XY: 2231 AN XY: 74426

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.: 30

Bravo AF: 0.0331

Asia WGS AF: 0.0170 AC: 58 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

Other links and lift over

dbSNP: rs78912482; hg19: chr7-28225811;