15-40370547-G-A

Variant names:

• chr15-40370547-G-A
• rs3803359
• NM_033510.3:c.*229G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 13 publications found

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]

LOC124903472 (HGNC:):

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033510.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DISP2	NM_033510.3	MANE Select	c.*229G>A		3_prime_UTR	Exon 8 of 8	NP_277045.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DISP2	ENST00000267889.5	TSL:1 MANE Select	c.*229G>A		3_prime_UTR	Exon 8 of 8	ENSP00000267889.3
	DISP2	ENST00000558623.1	TSL:3	n.75-65G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.178 AC: 26992 AN: 152000 Hom.: 2621 Cov.: 33

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.: 8 AF XY: 0.143 AC XY: 48618 AN XY: 339496

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

GnomAD4 genome AF: 0.178 AC: 27019 AN: 152118 Hom.: 2623 Cov.: 33 AF XY: 0.172 AC XY: 12769 AN XY: 74372

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: 48 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11086 AN: 67974

Other (OTH) AF: 0.166 AC: 350 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	8.1
DANN	Benign	0.76
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3803359; hg19: chr15-40662748;