11-64989295-C-T

Variant names:

• chr11-64989295-C-T
• NM_138456.4:c.659G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_138456.4(BATF2):​c.659G>A​(p.Gly220Glu) variant causes a missense 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. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: BATF2 NM_138456.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -2.64
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.03722641).

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.659G>A	p.Gly220Glu	missense	Exon 3 of 3	NP_612465.3
	BATF2	NM_001300807.2		c.587G>A	p.Gly196Glu	missense	Exon 2 of 2	NP_001287736.1	B4DV37
	BATF2	NM_001300808.2		c.404G>A	p.Gly135Glu	missense	Exon 2 of 2	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.659G>A	p.Gly220Glu	missense	Exon 3 of 3	ENSP00000301887.4	Q8N1L9-1
	BATF2	ENST00000435842.2	TSL:1	c.404G>A	p.Gly135Glu	missense	Exon 2 of 2	ENSP00000398911.2	Q8N1L9-2
	BATF2	ENST00000527716.1	TSL:2	c.587G>A	p.Gly196Glu	missense	Exon 2 of 2	ENSP00000434915.1	B4DV37

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.36	T
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.046
DANN	Benign	0.46
DEOGEN2	Benign	0.011	T
Eigen	Benign	-2.0
Eigen_PC	Benign	-2.1
FATHMM_MKL	Benign	0.0050	N
LIST_S2	Benign	0.56	T
M_CAP	Benign	0.0038	T
MetaRNN	Benign	0.037	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.69	N
PhyloP100		-2.6
PROVEAN	Benign	-1.6	N
REVEL	Benign	0.046
Sift	Benign	0.091	T
Sift4G	Benign	0.21	T
Polyphen		0.0	B
Vest4		0.038
MutPred		0.11		Gain of solvent accessibility (P = 0.0456)
MVP		0.20
MPC		0.057
ClinPred		0.071	T
GERP RS		-9.7
Varity_R		0.049
gMVP		0.10
Mutation Taster		=95/5	polymorphism

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

Other links and lift over

hg19: chr11-64756767;