rs1413477736

Variant names:

• chr18-54591232-C-A
• rs1413477736
• ENST00000321600.1:c.28C>A

Your query was ambiguous. Multiple possible variants found:

• chr18-54591232-C-A
• chr18-54591232-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001307955.1(DYNAP):​c.37C>A​(p.Gln13Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: DYNAP NM_001307955.1 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.618
• Publications: 0 publications found

Genes affected

DYNAP (HGNC:26808): (dynactin associated protein) Involved in several processes, including activation of protein kinase B activity; cellular response to ergosterol; and positive regulation of cell population proliferation. Located in Golgi apparatus and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.08440742).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001307955.1. 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
	DYNAP	NM_001307955.1		c.37C>A	p.Gln13Lys	missense	Exon 2 of 3	NP_001294884.1	K7EMN5
	DYNAP	NM_173629.3	MANE Select	c.-51C>A		upstream_gene	N/A	NP_775900.2	A0A3B3IRJ4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DYNAP	ENST00000321600.1	TSL:2	c.28C>A	p.Gln10Lys	missense	Exon 1 of 3	ENSP00000315265.1	Q8N1N2
	DYNAP	ENST00000585973.1	TSL:3	c.37C>A	p.Gln13Lys	missense	Exon 2 of 3	ENSP00000466577.1	K7EMN5
	DYNAP	ENST00000648945.2	MANE Select	c.-51C>A		upstream_gene	N/A	ENSP00000496812.1	A0A3B3IRJ4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

Alfa AF: 0.0000712 Hom.: 0

Bravo AF: 0.00000378

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.074
BayesDel_addAF	Benign	-0.25	T
BayesDel_noAF	Benign	-0.59
CADD	Benign	0.30
DANN	Benign	0.29
DEOGEN2	Benign	0.0071	T
Eigen	Benign	-0.75
Eigen_PC	Benign	-0.89
FATHMM_MKL	Benign	0.019	N
LIST_S2	Benign	0.45	T
M_CAP	Benign	0.011	T
MetaRNN	Benign	0.084	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.34	N
PhyloP100		-0.62
PrimateAI	Benign	0.26	T
PROVEAN	Benign	-0.39	N
REVEL	Benign	0.023
Sift	Pathogenic	0.0	D
Sift4G	Benign	0.33	T
Polyphen		0.78	P
Vest4		0.18
MutPred		0.19		Gain of ubiquitination at Q10 (P = 0.0198)
MVP		0.085
MPC		0.017
ClinPred		0.15	T
GERP RS		-1.8
PromoterAI		0.017	Neutral
Varity_R		0.098
gMVP		0.028
Mutation Taster		=98/2	polymorphism

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: rs1413477736; hg19: chr18-52258463;