11-64989276-AGG-CGT

Variant names:

• chr11-64989276-AGG-CGT
• NM_138456.4:c.676_678delCCTinsACG
• BATF2 p.Pro226Thr

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_138456.4(BATF2):​c.676_678delCCTinsACG​(p.Pro226Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P226A) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: BATF2 NM_138456.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432
• Publications: 0 publications found

Genes affected

BATF2 (HGNC:25163): (basic leucine zipper ATF-like transcription factor 2) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in defense response to protozoan; myeloid dendritic cell differentiation; and regulation of transcription by RNA polymerase II. Predicted to be part of chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138456.4. 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
	BATF2	NM_138456.4	MANE Select	c.676_678delCCTinsACG	p.Pro226Thr	missense	N/A	NP_612465.3
	BATF2	NM_001300807.2		c.604_606delCCTinsACG	p.Pro202Thr	missense	N/A	NP_001287736.1	B4DV37
	BATF2	NM_001300808.2		c.421_423delCCTinsACG	p.Pro141Thr	missense	N/A	NP_001287737.1	Q8N1L9-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BATF2	ENST00000301887.9	TSL:1 MANE Select	c.676_678delCCTinsACG	p.Pro226Thr	missense	N/A	ENSP00000301887.4	Q8N1L9-1
	BATF2	ENST00000435842.2	TSL:1	c.421_423delCCTinsACG	p.Pro141Thr	missense	N/A	ENSP00000398911.2	Q8N1L9-2
	BATF2	ENST00000527716.1	TSL:2	c.604_606delCCTinsACG	p.Pro202Thr	missense	N/A	ENSP00000434915.1	B4DV37

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.43

Splicing

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

hg19: chr11-64756748;