rs369396168

Variant names:

• chr17-7024228-C-A
• rs369396168
• NM_181844.4:c.325C>A

Your query was ambiguous. Multiple possible variants found:

• chr17-7024228-C-A
• chr17-7024228-C-G
• chr17-7024228-C-T

Variant summary

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

The NM_181844.4(BCL6B):​c.325C>A​(p.Pro109Thr) 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. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: BCL6B NM_181844.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.179

Genes affected

BCL6B (HGNC:1002): (BCL6B transcription repressor) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in several processes, including regulation of gene expression; regulation of inflammatory response; and type 2 immune response. Predicted to be located in nucleus. Predicted to be active in nucleoplasm. [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=0.21606475).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCL6B	NM_181844.4	c.325C>A	p.Pro109Thr	missense_variant	Exon 3 of 9	ENST00000293805.10	NP_862827.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCL6B	ENST00000293805.10	c.325C>A	p.Pro109Thr	missense_variant	Exon 3 of 9	1	NM_181844.4	ENSP00000293805.5
BCL6B	ENST00000576705.1	c.325C>A	p.Pro109Thr	missense_variant	Exon 3 of 3	4		ENSP00000460071.1
BCL6B	ENST00000573503.1	c.325C>A	p.Pro109Thr	missense_variant	Exon 2 of 2	2		ENSP00000460282.1
BCL6B	ENST00000572216.1	n.233C>A		non_coding_transcript_exon_variant	Exon 3 of 4	4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 39

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.49
BayesDel_addAF	Benign	-0.056	T
BayesDel_noAF	Benign	-0.32
CADD	Benign	22
DANN	Uncertain	1.0
DEOGEN2	Benign	0.23	T;.;.
Eigen	Benign	0.12
Eigen_PC	Benign	0.098
FATHMM_MKL	Benign	0.34	N
LIST_S2	Benign	0.81	T;D;T
M_CAP	Benign	0.018	T
MetaRNN	Benign	0.22	T;T;T
MetaSVM	Benign	-0.65	T
MutationAssessor	Benign	0.92	L;.;.
PrimateAI	Uncertain	0.63	T
PROVEAN	Benign	-0.62	N;.;.
REVEL	Benign	0.25
Sift	Benign	0.57	T;.;.
Sift4G	Benign	0.078	T;T;T
Polyphen		0.98	D;.;.
Vest4		0.15
MutPred		0.46		Gain of catalytic residue at P109 (P = 0.0235);Gain of catalytic residue at P109 (P = 0.0235);Gain of catalytic residue at P109 (P = 0.0235);
MVP		0.86
MPC		1.2
ClinPred		0.58	D
GERP RS		5.2
Varity_R		0.10
gMVP		0.39

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs369396168; hg19: chr17-6927547;