chr18-5978932-C-T

Variant names:

• chr18-5978932-C-T
• rs1539808
• NM_001330559.2:c.1445-9370G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001330559.2(L3MBTL4):​c.1445-9370G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.077 in 152,190 control chromosomes in the GnomAD database, including 852 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.077 (852 hom., cov: 32)
• Consequence: L3MBTL4 NM_001330559.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708
• Publications: 6 publications found

Genes affected

L3MBTL4 (HGNC:26677): (L3MBTL histone methyl-lysine binding protein 4) Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in negative regulation of transcription, DNA-templated. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000266846 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001330559.2. 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
	L3MBTL4	NM_001330559.2	MANE Select	c.1445-9370G>A		intron	N/A	NP_001317488.1
	L3MBTL4	NM_001365770.2		c.1472-9370G>A		intron	N/A	NP_001352699.1
	L3MBTL4	NM_173464.4		c.1472-9370G>A		intron	N/A	NP_775735.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	L3MBTL4	ENST00000317931.12	TSL:5 MANE Select	c.1445-9370G>A		intron	N/A	ENSP00000318543.7
	L3MBTL4	ENST00000955913.1		c.1478-9370G>A		intron	N/A	ENSP00000625972.1
	L3MBTL4	ENST00000400105.6	TSL:2	c.1472-9370G>A		intron	N/A	ENSP00000382976.2

Frequencies

GnomAD3 genomes AF: 0.0768 AC: 11673 AN: 152070 Hom.: 843 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.0448

Gnomad ASJ AF: 0.0476

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.0657

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0140

Gnomad OTH AF: 0.0569

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

GnomAD4 genome AF: 0.0770 AC: 11712 AN: 152190 Hom.: 852 Cov.: 32 AF XY: 0.0823 AC XY: 6126 AN XY: 74400

African (AFR) AF: 0.176 AC: 7322 AN: 41502

American (AMR) AF: 0.0447 AC: 684 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0476 AC: 165 AN: 3470

East Asian (EAS) AF: 0.147 AC: 756 AN: 5158

South Asian (SAS) AF: 0.193 AC: 931 AN: 4824

European-Finnish (FIN) AF: 0.0657 AC: 697 AN: 10602

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0140 AC: 952 AN: 68022

Other (OTH) AF: 0.0563 AC: 119 AN: 2114

Alfa AF: 0.0366 Hom.: 119

Bravo AF: 0.0764

Asia WGS AF: 0.148 AC: 513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.60
DANN	Benign	0.49
PhyloP100		-0.71
Mutation Taster		=100/0	polymorphism (auto)

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

dbSNP: rs1539808; hg19: chr18-5978931;