1-155015050-C-A

Variant names:

• chr1-155015050-C-A
• rs11264295
• NM_001256455.2:c.390C>A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001256455.2(ZBTB7B):​c.390C>A​(p.Ile130Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. I130I) has been classified as Benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ZBTB7B NM_001256455.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.72

Genes affected

ZBTB7B (HGNC:18668): (zinc finger and BTB domain containing 7B) This gene encodes a zinc finger-containing transcription factor that acts as a key regulator of lineage commitment of immature T-cell precursors. It is necessary and sufficient for commitment of CD4 lineage, while its absence causes CD8 commitment. It also functions as a transcriptional repressor of type I collagen genes. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2012]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZBTB7B	NM_001256455.2	c.390C>A	p.Ile130Ile	synonymous_variant	Exon 2 of 3	ENST00000535420.6	NP_001243384.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZBTB7B	ENST00000535420.6	c.390C>A	p.Ile130Ile	synonymous_variant	Exon 2 of 3	5	NM_001256455.2	ENSP00000438647.1
ZBTB7B	ENST00000292176.2	c.390C>A	p.Ile130Ile	synonymous_variant	Exon 1 of 2	1		ENSP00000292176.2
ZBTB7B	ENST00000368426.3	c.390C>A	p.Ile130Ile	synonymous_variant	Exon 3 of 4	1		ENSP00000357411.3
ZBTB7B	ENST00000417934.6	c.492C>A	p.Ile164Ile	synonymous_variant	Exon 4 of 5	2		ENSP00000406286.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 92

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	8.6
DANN	Benign	0.93
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

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

Publications

LitVar

Other links and lift over

dbSNP: rs11264295; hg19: chr1-154987526;