dbSNP rs3803359: DISP2:c.*229G>A (chr15-40370547-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_033510.3(DISP2):c.*229G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 792,362 control chromosomes in the GnomAD database, including 10,245 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 0.18 ( 2623 hom., cov: 33)

Exomes 𝑓: 0.15 ( 7622 hom. )

Consequence

DISP2
NM_033510.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.09

Publications

13 publications found

Variant links:

Genes affected

DISP2 (HGNC:19712): (dispatched RND transporter family member 2) This gene is one of two human homologs of a segment-polarity gene known as dispatched identified in Drosophila. The product of this gene may be required for normal Hedgehog (Hh) signaling during embryonic pattern formation. [provided by RefSeq, Jan 2017]

DISP2 links:

LOC124903472 (HGNC:):

LOC124903472 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=-0.76).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DISP2	NM_033510.3 link	c.*229G>A		3_prime_UTR_variant	Exon 8 of 8	ENST00000267889.5	NP_277045.1
LOC124903472	XR_007064597.1 link	n.2417+336C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DISP2	ENST00000267889.5 link	c.*229G>A		3_prime_UTR_variant	Exon 8 of 8	1	NM_033510.3	ENSP00000267889.3		A7MBM2
DISP2	ENST00000558623.1 link	n.75-65G>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes

AF:

0.178

AC:

26992

AN:

152000

Hom.:

2621

Cov.:

show subpopulations

Gnomad AFR

AF:

0.252

Gnomad AMI

AF:

0.147

Gnomad AMR

AF:

0.116

Gnomad ASJ

AF:

0.156

Gnomad EAS

AF:

0.123

Gnomad SAS

AF:

0.0823

Gnomad FIN

AF:

0.152

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.163

Gnomad OTH

AF:

0.166

GnomAD4 exome

AF:

0.147

AC:

94369

AN:

640244

Hom.:

7622

Cov.:

AF XY:

0.143

AC XY:

48618

AN XY:

339496

show subpopulations

African (AFR)

AF:

0.261

AC:

4554

AN:

17424

American (AMR)

AF:

0.0868

AC:

2955

AN:

34052

Ashkenazi Jewish (ASJ)

AF:

0.147

AC:

2971

AN:

20232

East Asian (EAS)

AF:

0.121

AC:

3776

AN:

31174

South Asian (SAS)

AF:

0.0730

AC:

4647

AN:

63652

European-Finnish (FIN)

AF:

0.144

AC:

4567

AN:

31632

Middle Eastern (MID)

AF:

0.136

AC:

571

AN:

4204

European-Non Finnish (NFE)

AF:

0.161

AC:

64998

AN:

404632

Other (OTH)

AF:

0.160

AC:

5330

AN:

33242

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

3990

7980

11971

15961

19951

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1048

2096

3144

4192

5240

<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:

0.178

AC:

27019

AN:

152118

Hom.:

2623

Cov.:

AF XY:

0.172

AC XY:

12769

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.252

AC:

10443

AN:

41474

American (AMR)

AF:

0.116

AC:

1773

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.156

AC:

542

AN:

3472

East Asian (EAS)

AF:

0.123

AC:

638

AN:

5182

South Asian (SAS)

AF:

0.0821

AC:

396

AN:

4822

European-Finnish (FIN)

AF:

0.152

AC:

1609

AN:

10584

Middle Eastern (MID)

AF:

0.163

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.163

AC:

11086

AN:

67974

Other (OTH)

AF:

0.166

AC:

350

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1120

2240

3359

4479

5599

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

284

568

852

1136

1420

<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:

0.160

Hom.:

714

Bravo

AF:

0.180

Asia WGS

AF:

0.131

AC:

453

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

8.1

(source)

DANN

Benign

0.76

PhyloP100

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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