chr1-11516149-C-T

Variant names:

• chr1-11516149-C-T
• rs17036950
• NM_020780.2:c.1737C>T

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_Moderate BP6_Very_Strong BP7 BA1

The NM_020780.2(DISP3):​c.1737C>T​(p.Asn579Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00377 in 1,613,980 control chromosomes in the GnomAD database, including 141 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.017 (62 hom., cov: 32)
  • Exomes 𝑓: 0.0023 (79 hom.)
• Consequence: DISP3 NM_020780.2 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 1.19
• Publications: 4 publications found

Genes affected

DISP3 (HGNC:29251): (dispatched RND transporter family member 3) Involved in negative regulation of neuron differentiation; positive regulation of lipid metabolic process; and positive regulation of neural precursor cell proliferation. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -19 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BP6: Variant 1-11516149-C-T is Benign according to our data. Variant chr1-11516149-C-T is described in ClinVar as Benign. ClinVar VariationId is 775509.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=1.19 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0562 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020780.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DISP3	NM_020780.2	MANE Select	c.1737C>T	p.Asn579Asn	synonymous	Exon 6 of 21	NP_065831.1	Q9P2K9-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DISP3	ENST00000294484.7	TSL:1 MANE Select	c.1737C>T	p.Asn579Asn	synonymous	Exon 6 of 21	ENSP00000294484.6	Q9P2K9-1
	DISP3	ENST00000922105.1		c.1737C>T	p.Asn579Asn	synonymous	Exon 6 of 21	ENSP00000592164.1
	DISP3	ENST00000922103.1		c.1737C>T	p.Asn579Asn	synonymous	Exon 6 of 21	ENSP00000592162.1

Frequencies

GnomAD3 genomes AF: 0.0175 AC: 2658 AN: 152198 Hom.: 61 Cov.: 32

Gnomad AFR AF: 0.0582

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00745

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0139

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000323

Gnomad OTH AF: 0.0167

GnomAD2 exomes AF: 0.00536 AC: 1336 AN: 249060 AF XY: 0.00416

Gnomad AFR exome AF: 0.0606

Gnomad AMR exome AF: 0.00302

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0126

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000248

Gnomad OTH exome AF: 0.00380

GnomAD4 exome AF: 0.00235 AC: 3429 AN: 1461664 Hom.: 79 Cov.: 31 AF XY: 0.00208 AC XY: 1510 AN XY: 727154

African (AFR) AF: 0.0645 AC: 2158 AN: 33480

American (AMR) AF: 0.00351 AC: 157 AN: 44714

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26108

East Asian (EAS) AF: 0.0147 AC: 582 AN: 39698

South Asian (SAS) AF: 0.000417 AC: 36 AN: 86240

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53410

Middle Eastern (MID) AF: 0.00503 AC: 29 AN: 5768

European-Non Finnish (NFE) AF: 0.000132 AC: 147 AN: 1111860

Other (OTH) AF: 0.00530 AC: 320 AN: 60386

GnomAD4 genome AF: 0.0175 AC: 2661 AN: 152316 Hom.: 62 Cov.: 32 AF XY: 0.0168 AC XY: 1252 AN XY: 74482

African (AFR) AF: 0.0581 AC: 2415 AN: 41550

American (AMR) AF: 0.00745 AC: 114 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3466

East Asian (EAS) AF: 0.0139 AC: 72 AN: 5178

South Asian (SAS) AF: 0.000414 AC: 2 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10626

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.000323 AC: 22 AN: 68036

Other (OTH) AF: 0.0165 AC: 35 AN: 2116

Alfa AF: 0.00660 Hom.: 35

Bravo AF: 0.0205

Asia WGS AF: 0.00462 AC: 16 AN: 3478

EpiCase AF: 0.000545

EpiControl AF: 0.000356

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	6.3
DANN	Benign	0.61
PhyloP100		1.2
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs17036950; hg19: chr1-11576206; COSMIC: COSV53837646;