rs9660296

Variant names:

• chr1-32642799-T-C
• rs9660296
• NM_178547.5:c.97+7634A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_178547.5(ZBTB8OS):​c.97+7634A>G variant causes a intron change. 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 0.93 (1492 hom., cov: 4)
• Consequence: ZBTB8OS NM_178547.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 2 publications found

Genes affected

ZBTB8OS (HGNC:24094): (zinc finger and BTB domain containing 8 opposite strand) Predicted to enable metal ion binding activity. Involved in tRNA splicing, via endonucleolytic cleavage and ligation. Part of tRNA-splicing ligase complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.962 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178547.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZBTB8OS	NM_178547.5	MANE Select	c.97+7634A>G		intron	N/A	NP_848642.2	Q8IWT0-1
	ZBTB8OS	NM_001366264.1		c.133+7634A>G		intron	N/A	NP_001353193.1
	ZBTB8OS	NM_001308135.2		c.137+7630A>G		intron	N/A	NP_001295064.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZBTB8OS	ENST00000468695.6	TSL:1 MANE Select	c.97+7634A>G		intron	N/A	ENSP00000417677.2	Q8IWT0-1
	ZBTB8OS	ENST00000436661.6	TSL:1	c.97+7634A>G		intron	N/A	ENSP00000413485.2	Q8IWT0-2
	ZBTB8OS	ENST00000341885.6	TSL:1	c.97+7634A>G		intron	N/A	ENSP00000343760.6	F6SII6

Frequencies

GnomAD3 genomes AF: 0.927 AC: 2985 AN: 3220 Hom.: 1489 Cov.: 4

Gnomad AFR AF: 0.667

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.978

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 1.00

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.958

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

GnomAD4 genome AF: 0.927 AC: 2991 AN: 3228 Hom.: 1492 Cov.: 4 AF XY: 0.927 AC XY: 1333 AN XY: 1438

African (AFR) AF: 0.665 AC: 456 AN: 686

American (AMR) AF: 0.978 AC: 182 AN: 186

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 98 AN: 98

East Asian (EAS) AF: 1.00 AC: 116 AN: 116

South Asian (SAS) AF: 1.00 AC: 52 AN: 52

European-Finnish (FIN) AF: 1.00 AC: 118 AN: 118

Middle Eastern (MID) AF: 1.00 AC: 10 AN: 10

European-Non Finnish (NFE) AF: 0.999 AC: 1885 AN: 1886

Other (OTH) AF: 0.960 AC: 48 AN: 50

Alfa AF: 0.974 Hom.: 5630

Bravo AF: 0.965

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.35
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9660296;

hg19: chr1-33108400;