GeneBe

rs7916571

Variant names:

Variant summary

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

The ENST00000439464.6(DMBT1L1):​n.2774-24T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 152,402 control chromosomes in the GnomAD database, including 28,876 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 0.61 ( 28775 hom., cov: 31)
Exomes 𝑓: 0.69 ( 101 hom. )

Consequence

DMBT1L1
ENST00000439464.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.90

Publications

2 publications found
Variant links:
Genes affected
DMBT1L1 (HGNC:49497): (deleted in malignant brain tumors 1 like 1 (pseudogene))

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=-0.86).
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
DMBT1L1NR_003570.2 linkn.2774-24T>A intron_variant Intron 23 of 27

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DMBT1L1ENST00000439464.6 linkn.2774-24T>A intron_variant Intron 23 of 27 2
DMBT1L1ENST00000636837.3 linkn.3615-24T>A intron_variant Intron 15 of 23 6

Frequencies

GnomAD3 genomes
AF:
0.614
AC:
93255
AN:
151856
Hom.:
28769
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.534
Gnomad AMI
AF:
0.609
Gnomad AMR
AF:
0.626
Gnomad ASJ
AF:
0.625
Gnomad EAS
AF:
0.552
Gnomad SAS
AF:
0.732
Gnomad FIN
AF:
0.638
Gnomad MID
AF:
0.699
Gnomad NFE
AF:
0.652
Gnomad OTH
AF:
0.616
GnomAD4 exome
AF:
0.689
AC:
295
AN:
428
Hom.:
101
Cov.:
0
AF XY:
0.695
AC XY:
178
AN XY:
256
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
0.690
AC:
290
AN:
420
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.500
AC:
1
AN:
2
Other (OTH)
AF:
0.667
AC:
4
AN:
6
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.481
Heterozygous variant carriers
0
5
10
14
19
24
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
AF:
0.614
AC:
93298
AN:
151974
Hom.:
28775
Cov.:
31
AF XY:
0.616
AC XY:
45725
AN XY:
74282
show subpopulations
African (AFR)
AF:
0.533
AC:
22087
AN:
41428
American (AMR)
AF:
0.626
AC:
9564
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
0.625
AC:
2171
AN:
3472
East Asian (EAS)
AF:
0.551
AC:
2833
AN:
5142
South Asian (SAS)
AF:
0.732
AC:
3527
AN:
4818
European-Finnish (FIN)
AF:
0.638
AC:
6732
AN:
10552
Middle Eastern (MID)
AF:
0.707
AC:
208
AN:
294
European-Non Finnish (NFE)
AF:
0.652
AC:
44323
AN:
67976
Other (OTH)
AF:
0.617
AC:
1298
AN:
2104
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1865
3729
5594
7458
9323
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
782
1564
2346
3128
3910
<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:
0.456
Hom.:
1002
Bravo
AF:
0.606

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.025
DANN
Benign
0.48
PhyloP100
-1.9

Splicing

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

Publications

Other links and lift over

dbSNP: rs7916571; hg19: chr10-124551779; COSMIC: COSV71563453; API