chr15-40370547-G-A

Position:

• chr15-40370547-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000267889.5(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 ENST00000267889.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
DISP2	NM_033510.3	c.*229G>A		3_prime_UTR_variant	8/8	ENST00000267889.5	NP_277045.1
LOC124903472	XR_007064597.1	n.2417+336C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DISP2	ENST00000267889.5	c.*229G>A		3_prime_UTR_variant	8/8	1	NM_033510.3	ENSP00000267889	P1
DISP2	ENST00000558623.1	n.75-65G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR exome AF: 0.261

Gnomad4 AMR exome AF: 0.0868

Gnomad4 ASJ exome AF: 0.147

Gnomad4 EAS exome AF: 0.121

Gnomad4 SAS exome AF: 0.0730

Gnomad4 FIN exome AF: 0.144

Gnomad4 NFE exome AF: 0.161

Gnomad4 OTH exome AF: 0.160

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

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.0821

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.166

Alfa AF: 0.159 Hom.: 637

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
DANN	Benign	0.76

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

LitVar

Other links and lift over

dbSNP: rs3803359; hg19: chr15-40662748;