19-7051382-A-G

Position:

• chr19-7051382-A-G

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

The ENST00000381393.3(MBD3L2):​c.387A>G​(p.Arg129=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0019 (0 hom., cov: 21)
  • Exomes 𝑓: 0.0038 (61 hom.)
  • Failed GnomAD Quality Control
• Consequence: MBD3L2 ENST00000381393.3 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.28

Genes affected

MBD3L2 (HGNC:18532): (methyl-CpG binding domain protein 3 like 2) This gene encodes a protein that is related to methyl-CpG-binding proteins but lacks the methyl-CpG binding domain. The protein has been found in germ cell tumors and some somatic tissues. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -7 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.11).
• BP6: Variant 19-7051382-A-G is Benign according to our data. Variant chr19-7051382-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2649148.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-1.28 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MBD3L2	NM_144614.4	c.387A>G	p.Arg129=	synonymous_variant	2/2	ENST00000381393.3	NP_653215.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MBD3L2	ENST00000381393.3	c.387A>G	p.Arg129=	synonymous_variant	2/2	1	NM_144614.4	ENSP00000370800	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 263 AN: 134868 Hom.: 0 Cov.: 21 FAILED QC

Gnomad AFR AF: 0.00398

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000843

Gnomad ASJ AF: 0.000943

Gnomad EAS AF: 0.00132

Gnomad SAS AF: 0.000543

Gnomad FIN AF: 0.000211

Gnomad MID AF: 0.00338

Gnomad NFE AF: 0.00141

Gnomad OTH AF: 0.00225

GnomAD3 exomes AF: 0.00322 AC: 306 AN: 94962 Hom.: 11 AF XY: 0.00318 AC XY: 159 AN XY: 49934

Gnomad AFR exome AF: 0.00555

Gnomad AMR exome AF: 0.00281

Gnomad ASJ exome AF: 0.00170

Gnomad EAS exome AF: 0.00249

Gnomad SAS exome AF: 0.00378

Gnomad FIN exome AF: 0.000610

Gnomad NFE exome AF: 0.00350

Gnomad OTH exome AF: 0.00403

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00379 AC: 1933 AN: 510038 Hom.: 61 Cov.: 0 AF XY: 0.00400 AC XY: 1092 AN XY: 272954

Gnomad4 AFR exome AF: 0.00481

Gnomad4 AMR exome AF: 0.00494

Gnomad4 ASJ exome AF: 0.00144

Gnomad4 EAS exome AF: 0.00243

Gnomad4 SAS exome AF: 0.00551

Gnomad4 FIN exome AF: 0.000764

Gnomad4 NFE exome AF: 0.00403

Gnomad4 OTH exome AF: 0.00321

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00195 AC: 263 AN: 134976 Hom.: 0 Cov.: 21 AF XY: 0.00199 AC XY: 130 AN XY: 65206

Gnomad4 AFR AF: 0.00396

Gnomad4 AMR AF: 0.000842

Gnomad4 ASJ AF: 0.000943

Gnomad4 EAS AF: 0.00132

Gnomad4 SAS AF: 0.000544

Gnomad4 FIN AF: 0.000211

Gnomad4 NFE AF: 0.00141

Gnomad4 OTH AF: 0.00222

Alfa AF: 0.00247 Hom.: 7

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2024

MBD3L2: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	3.1
DANN	Benign	0.23

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: rs754556726; hg19: chr19-7051393;