11-64989803-A-G

Variant names:

• chr11-64989803-A-G
• NM_138456.4:c.151T>C

Variant summary

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

The NM_138456.4(BATF2):​c.151T>C​(p.Ser51Pro) 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. 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: 0.168

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

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 (MetaRNN=0.25612915).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BATF2	NM_138456.4	c.151T>C	p.Ser51Pro	missense_variant	Exon 3 of 3	ENST00000301887.9	NP_612465.3
BATF2	NM_001300807.2	c.79T>C	p.Ser27Pro	missense_variant	Exon 2 of 2		NP_001287736.1
BATF2	NM_001300808.2	c.-105T>C		5_prime_UTR_variant	Exon 2 of 2		NP_001287737.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BATF2	ENST00000301887.9	c.151T>C	p.Ser51Pro	missense_variant	Exon 3 of 3	1	NM_138456.4	ENSP00000301887.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Apr 29, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.151T>C (p.S51P) alteration is located in exon 3 (coding exon 3) of the BATF2 gene. This alteration results from a T to C substitution at nucleotide position 151, causing the serine (S) at amino acid position 51 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.93
BayesDel_addAF	Benign	-0.10	T
BayesDel_noAF	Benign	-0.38
CADD	Benign	17
DANN	Uncertain	0.98
DEOGEN2	Benign	0.11	T;T;.
Eigen	Benign	-0.60
Eigen_PC	Benign	-0.79
FATHMM_MKL	Benign	0.026	N
LIST_S2	Benign	0.23	T;T;T
M_CAP	Benign	0.027	D
MetaRNN	Benign	0.26	T;T;T
MetaSVM	Benign	-0.99	T
MutationAssessor	Uncertain	2.3	M;.;.
PROVEAN	Uncertain	-2.9	D;D;D
REVEL	Benign	0.083
Sift	Benign	0.052	T;D;T
Sift4G	Benign	0.22	T;T;T
Polyphen		0.77	P;.;.
Vest4		0.27
MutPred		0.59		Loss of phosphorylation at S51 (P = 0.0484);.;.;
MVP		0.67
MPC		0.28
ClinPred		0.76	D
GERP RS		-0.49
Varity_R		0.38
gMVP		0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-64757275;