Genetic Variant ENST00000439464.6:n.746+59C>T (chr10-122769414-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.746+59C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 152,360 control chromosomes in the GnomAD database, including 21,262 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 0.53 ( 21203 hom., cov: 31)

Exomes 𝑓: 0.55 ( 59 hom. )

Consequence

DMBT1L1
ENST00000439464.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.207

Publications

4 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=-1.02).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DMBT1L1	NR_003570.2 link	n.746+59C>T		intron_variant	Intron 8 of 27

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DMBT1L1	ENST00000439464.6 link	n.746+59C>T		intron_variant	Intron 8 of 27	2
DMBT1L1	ENST00000636837.3 link	n.1885+1034C>T		intron_variant	Intron 6 of 23	6

Frequencies

GnomAD3 genomes

AF:

0.528

AC:

80201

AN:

151808

Hom.:

21193

Cov.:

show subpopulations

Gnomad AFR

AF:

0.536

Gnomad AMI

AF:

0.404

Gnomad AMR

AF:

0.538

Gnomad ASJ

AF:

0.456

Gnomad EAS

AF:

0.433

Gnomad SAS

AF:

0.565

Gnomad FIN

AF:

0.528

Gnomad MID

AF:

0.465

Gnomad NFE

AF:

0.532

Gnomad OTH

AF:

0.548

GnomAD4 exome

AF:

0.550

AC:

240

AN:

436

Hom.:

AF XY:

0.550

AC XY:

144

AN XY:

262

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.547

AC:

233

AN:

426

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.667

AC:

AN:

Other (OTH)

AF:

0.750

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

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:

0.528

AC:

80250

AN:

151924

Hom.:

21203

Cov.:

AF XY:

0.525

AC XY:

38940

AN XY:

74212

show subpopulations

African (AFR)

AF:

0.536

AC:

22195

AN:

41434

American (AMR)

AF:

0.537

AC:

8213

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.456

AC:

1578

AN:

3464

East Asian (EAS)

AF:

0.433

AC:

2230

AN:

5154

South Asian (SAS)

AF:

0.563

AC:

2702

AN:

4802

European-Finnish (FIN)

AF:

0.528

AC:

5555

AN:

10526

Middle Eastern (MID)

AF:

0.466

AC:

135

AN:

290

European-Non Finnish (NFE)

AF:

0.532

AC:

36118

AN:

67952

Other (OTH)

AF:

0.547

AC:

1158

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1937

3875

5812

7750

9687

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

708

1416

2124

2832

3540

<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:

0.531

Hom.:

36472

Bravo

AF:

0.526

Asia WGS

AF:

0.478

AC:

1665

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.42

(source)

DANN

Benign

0.17

PhyloP100

-0.21

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