7-28186192-C-T

Variant names:

• chr7-28186192-C-T
• rs78912482
• ENST00000444500.3:n.180+440C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000444500.3(JAZF1-AS1):​n.180+440C>T variant causes a intron 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 ENST00000444500.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.01
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 108 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
JAZF1-AS1	NR_034097.1	n.166+440C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JAZF1-AS1	ENST00000444500.3	n.180+440C>T		intron_variant	Intron 2 of 4	1
JAZF1-AS1	ENST00000436758.2	n.202+440C>T		intron_variant	Intron 2 of 3	2
JAZF1-AS1	ENST00000455963.6	n.301+440C>T		intron_variant	Intron 2 of 2	2

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

African (AFR) AF: 0.00992 AC: 412 AN: 41520

American (AMR) AF: 0.0363 AC: 555 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0429 AC: 149 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5188

South Asian (SAS) AF: 0.0311 AC: 150 AN: 4824

European-Finnish (FIN) AF: 0.0104 AC: 110 AN: 10586

Middle Eastern (MID) AF: 0.0651 AC: 19 AN: 292

European-Non Finnish (NFE) AF: 0.0495 AC: 3365 AN: 68012

Other (OTH) AF: 0.0531 AC: 112 AN: 2110

Alfa AF: 0.0291 Hom.: 35

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
PhyloP100		-5.0

Splicing

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

Other links and lift over

dbSNP: rs78912482; hg19: chr7-28225811;