Genetic Variant XM_047426130.1:c.1432T>C (chr10-122826317-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XM_047426130.1(LOC124900290):c.1432T>C(p.Trp478Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 985,776 control chromosomes in the GnomAD database, including 25,199 homozygotes. In-silico tool predicts a benign outcome for this variant. 4/4 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.21 ( 3617 hom., cov: 32)

Exomes 𝑓: 0.23 ( 21582 hom. )

Consequence

LOC124900290
XM_047426130.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.14

Publications

5 publications found

Variant links:

Genes affected

LOC124900290 (HGNC:):

LOC124900290 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=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900290	XM_047426130.1 link	c.1432T>C	p.Trp478Arg	missense_variant	Exon 8 of 8		XP_047282086.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000293396	ENST00000442370.6 link	n.1012T>C	non_coding_transcript_exon_variant	Exon 5 of 5	2
DMBT1L1	ENST00000636837.3 link	n.5693T>C	non_coding_transcript_exon_variant	Exon 24 of 24	6
ENSG00000293396	ENST00000728123.1 link	n.758T>C	non_coding_transcript_exon_variant	Exon 5 of 5
ENSG00000293396	ENST00000728124.1 link	n.999T>C	non_coding_transcript_exon_variant	Exon 5 of 5

Frequencies

GnomAD3 genomes

AF:

0.214

AC:

32540

AN:

152044

Hom.:

3613

Cov.:

show subpopulations

Gnomad AFR

AF:

0.155

Gnomad AMI

AF:

0.263

Gnomad AMR

AF:

0.263

Gnomad ASJ

AF:

0.229

Gnomad EAS

AF:

0.295

Gnomad SAS

AF:

0.148

Gnomad FIN

AF:

0.272

Gnomad MID

AF:

0.158

Gnomad NFE

AF:

0.227

Gnomad OTH

AF:

0.218

GnomAD4 exome

AF:

0.226

AC:

188205

AN:

833612

Hom.:

21582

Cov.:

AF XY:

0.225

AC XY:

86742

AN XY:

385040

show subpopulations

African (AFR)

AF:

0.153

AC:

2421

AN:

15786

American (AMR)

AF:

0.247

AC:

243

AN:

982

Ashkenazi Jewish (ASJ)

AF:

0.232

AC:

1196

AN:

5152

East Asian (EAS)

AF:

0.302

AC:

1097

AN:

3630

South Asian (SAS)

AF:

0.153

AC:

2518

AN:

16460

European-Finnish (FIN)

AF:

0.259

AC:

186

AN:

718

Middle Eastern (MID)

AF:

0.160

AC:

259

AN:

1620

European-Non Finnish (NFE)

AF:

0.229

AC:

174107

AN:

761936

Other (OTH)

AF:

0.226

AC:

6178

AN:

27328

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.476

Heterozygous variant carriers

7485

14970

22456

29941

37426

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8146

16292

24438

32584

40730

<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:

0.214

AC:

32564

AN:

152164

Hom.:

3617

Cov.:

AF XY:

0.216

AC XY:

16034

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.155

AC:

6443

AN:

41536

American (AMR)

AF:

0.263

AC:

4019

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.229

AC:

794

AN:

3470

East Asian (EAS)

AF:

0.296

AC:

1529

AN:

5162

South Asian (SAS)

AF:

0.148

AC:

714

AN:

4822

European-Finnish (FIN)

AF:

0.272

AC:

2879

AN:

10580

Middle Eastern (MID)

AF:

0.167

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.227

AC:

15439

AN:

67994

Other (OTH)

AF:

0.217

AC:

458

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1294

2589

3883

5178

6472

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

344

688

1032

1376

1720

<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:

0.205

Hom.:

2751

Bravo

AF:

0.213

Asia WGS

AF:

0.226

AC:

783

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

(source)

DANN

Benign

0.68

PhyloP100

1.1

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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