Genetic Variant DMBT1L1:n.1239C>T (chr10-122777744-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000439464.6(DMBT1L1):n.1239C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 153,238 control chromosomes in the GnomAD database, including 25,600 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 0.58 ( 25362 hom., cov: 33)

Exomes 𝑓: 0.63 ( 238 hom. )

Consequence

DMBT1L1
ENST00000439464.6 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.822

Publications

2 publications found

Variant links:

Genes affected

DMBT1L1 (HGNC:):

DMBT1L1 links:

DMBT1L1 (HGNC:49497): (deleted in malignant brain tumors 1 like 1 (pseudogene))

DMBT1L1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DMBT1L1	NR_003570.2 link	n.1239C>T		non_coding_transcript_exon_variant	Exon 14 of 28

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DMBT1L1	ENST00000439464.6 link	n.1239C>T		non_coding_transcript_exon_variant	Exon 14 of 28	2
DMBT1L1	ENST00000636837.3 link	n.2234C>T		non_coding_transcript_exon_variant	Exon 9 of 24	6

Frequencies

GnomAD3 genomes

AF:

0.577

AC:

87705

AN:

151972

Hom.:

25353

Cov.:

show subpopulations

Gnomad AFR

AF:

0.518

Gnomad AMI

AF:

0.455

Gnomad AMR

AF:

0.602

Gnomad ASJ

AF:

0.618

Gnomad EAS

AF:

0.554

Gnomad SAS

AF:

0.732

Gnomad FIN

AF:

0.547

Gnomad MID

AF:

0.665

Gnomad NFE

AF:

0.602

Gnomad OTH

AF:

0.589

GnomAD4 exome

AF:

0.625

AC:

719

AN:

1150

Hom.:

238

Cov.:

AF XY:

0.625

AC XY:

519

AN XY:

830

show subpopulations

African (AFR)

AF:

0.600

AC:

AN:

American (AMR)

AF:

0.714

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.569

AC:

272

AN:

478

Middle Eastern (MID)

AF:

0.900

AC:

AN:

European-Non Finnish (NFE)

AF:

0.670

AC:

363

AN:

542

Other (OTH)

AF:

0.739

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.577

AC:

87750

AN:

152088

Hom.:

25362

Cov.:

AF XY:

0.579

AC XY:

43016

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.517

AC:

21467

AN:

41484

American (AMR)

AF:

0.602

AC:

9210

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.618

AC:

2140

AN:

3462

East Asian (EAS)

AF:

0.553

AC:

2850

AN:

5154

South Asian (SAS)

AF:

0.732

AC:

3532

AN:

4824

European-Finnish (FIN)

AF:

0.547

AC:

5782

AN:

10576

Middle Eastern (MID)

AF:

0.673

AC:

198

AN:

294

European-Non Finnish (NFE)

AF:

0.602

AC:

40910

AN:

67984

Other (OTH)

AF:

0.591

AC:

1248

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1923

3847

5770

7694

9617

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

760

1520

2280

3040

3800

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.519

Hom.:

2353

Bravo

AF:

0.574

Asia WGS

AF:

0.648

AC:

2258

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

(source)

DANN

Benign

0.42

PhyloP100

0.82

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over