11-118901807-T-C

Variant names:

• chr11-118901807-T-C
• rs34752197
• NM_001378213.1:c.1936A>G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001378213.1(BCL9L):​c.1936A>G​(p.Met646Val) variant causes a missense change. The variant allele was found at a frequency of 0.0115 in 1,610,672 control chromosomes in the GnomAD database, including 398 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.013 (53 hom., cov: 32)
  • Exomes 𝑓: 0.011 (345 hom.)
• Consequence: BCL9L NM_001378213.1 missense
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 5.54

Genes affected

BCL9L (HGNC:23688): (BCL9 like) Enables beta-catenin binding activity. Involved in several processes, including negative regulation of transforming growth factor beta receptor signaling pathway; positive regulation of epithelial to mesenchymal transition; and positive regulation of transcription by RNA polymerase II. Located in nucleolus and nucleoplasm. Part of beta-catenin-TCF complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0014236867).
• BP6: Variant 11-118901807-T-C is Benign according to our data. Variant chr11-118901807-T-C is described in ClinVar as [Benign]. Clinvar id is 402416.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCL9L	NM_001378213.1	c.1936A>G	p.Met646Val	missense_variant	Exon 8 of 10	ENST00000683865.1	NP_001365142.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCL9L	ENST00000683865.1	c.1936A>G	p.Met646Val	missense_variant	Exon 8 of 10		NM_001378213.1	ENSP00000507778.1
BCL9L	ENST00000334801.7	c.1936A>G	p.Met646Val	missense_variant	Exon 6 of 8	1		ENSP00000335320.3
BCL9L	ENST00000526143.2	c.1825A>G	p.Met609Val	missense_variant	Exon 6 of 8	5		ENSP00000482938.1
BCL9L	ENST00000530293.1	n.41-1046A>G		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.0127 AC: 1928 AN: 152150 Hom.: 53 Cov.: 32

Gnomad AFR AF: 0.00222

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00602

Gnomad ASJ AF: 0.00547

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.0166

Gnomad FIN AF: 0.0491

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00762

Gnomad OTH AF: 0.00863

GnomAD3 exomes AF: 0.0193 AC: 4826 AN: 250482 Hom.: 208 AF XY: 0.0190 AC XY: 2570 AN XY: 135418

Gnomad AFR exome AF: 0.00296

Gnomad AMR exome AF: 0.00235

Gnomad ASJ exome AF: 0.00481

Gnomad EAS exome AF: 0.128

Gnomad SAS exome AF: 0.0162

Gnomad FIN exome AF: 0.0436

Gnomad NFE exome AF: 0.00692

Gnomad OTH exome AF: 0.0116

GnomAD4 exome AF: 0.0114 AC: 16656 AN: 1458404 Hom.: 345 Cov.: 36 AF XY: 0.0116 AC XY: 8438 AN XY: 724794

Gnomad4 AFR exome AF: 0.00138

Gnomad4 AMR exome AF: 0.00278

Gnomad4 ASJ exome AF: 0.00353

Gnomad4 EAS exome AF: 0.0910

Gnomad4 SAS exome AF: 0.0163

Gnomad4 FIN exome AF: 0.0416

Gnomad4 NFE exome AF: 0.00745

Gnomad4 OTH exome AF: 0.0148

GnomAD4 genome AF: 0.0126 AC: 1925 AN: 152268 Hom.: 53 Cov.: 32 AF XY: 0.0149 AC XY: 1111 AN XY: 74456

Gnomad4 AFR AF: 0.00221

Gnomad4 AMR AF: 0.00601

Gnomad4 ASJ AF: 0.00547

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.0166

Gnomad4 FIN AF: 0.0491

Gnomad4 NFE AF: 0.00762

Gnomad4 OTH AF: 0.00854

Alfa AF: 0.00976 Hom.: 54

Bravo AF: 0.00937

TwinsUK AF: 0.00701 AC: 26

ALSPAC AF: 0.00519 AC: 20

ESP6500AA AF: 0.00432 AC: 19

ESP6500EA AF: 0.00722 AC: 62

ExAC AF: 0.0176 AC: 2140

Asia WGS AF: 0.0500 AC: 174 AN: 3478

EpiCase AF: 0.00611

EpiControl AF: 0.00599

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

not provided Benign:1

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.060
BayesDel_addAF	Benign	-0.42	T
BayesDel_noAF	Benign	-0.28
CADD	Benign	17
DANN	Benign	0.90
DEOGEN2	Benign	0.19	T;.
Eigen	Benign	-0.33
Eigen_PC	Benign	-0.18
FATHMM_MKL	Benign	0.67	D
LIST_S2	Benign	0.59	T;T
MetaRNN	Benign	0.0014	T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.2	L;.
PrimateAI	Benign	0.37	T
PROVEAN	Benign	-0.45	N;.
REVEL	Benign	0.14
Sift	Benign	0.051	T;.
Sift4G	Benign	0.59	T;T
Polyphen		0.0	B;.
Vest4		0.40
MPC		0.20
ClinPred		0.012	T
GERP RS		3.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2
Varity_R		0.10
gMVP		0.33

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: rs34752197; hg19: chr11-118772516;